WorldWideScience

Sample records for 15n backbone chemical

  1. Combining ambiguous chemical shift mapping with structure-based backbone and NOE assignment from 15N-NOESY

    Jang, Richard

    2011-01-01

    Chemical shift mapping is an important technique in NMRbased drug screening for identifying the atoms of a target protein that potentially bind to a drug molecule upon the molecule\\'s introduction in increasing concentrations. The goal is to obtain a mapping of peaks with known residue assignment from the reference spectrum of the unbound protein to peaks with unknown assignment in the target spectrum of the bound protein. Although a series of perturbed spectra help to trace a path from reference peaks to target peaks, a one-to-one mapping generally is not possible, especially for large proteins, due to errors, such as noise peaks, missing peaks, missing but then reappearing, overlapped, and new peaks not associated with any peaks in the reference. Due to these difficulties, the mapping is typically done manually or semi-automatically. However, automated methods are necessary for high-throughput drug screening. We present PeakWalker, a novel peak walking algorithm for fast-exchange systems that models the errors explicitly and performs many-to-one mapping. On the proteins: hBclXL, UbcH5B, and histone H1, it achieves an average accuracy of over 95% with less than 1.5 residues predicted per target peak. Given these mappings as input, we present PeakAssigner, a novel combined structure-based backbone resonance and NOE assignment algorithm that uses just 15N-NOESY, while avoiding TOCSY experiments and 13C- labeling, to resolve the ambiguities for a one-toone mapping. On the three proteins, it achieves an average accuracy of 94% or better. Copyright © 2011 ACM.

  2. Backbone and Ile-δ1, Leu, Val Methyl 1H, 13C and 15N NMR chemical shift assignments for human interferon-stimulated gene 15 protein

    Yin, Cuifeng; Aramini, James M.; Ma, LiChung; Cort, John R.; Swapna, G.V.T.; Krug, R. M.; Montelione, Gaetano

    2011-10-01

    Human interferon-stimulated gene 15 protein (ISG15), also called ubiquitin cross-reactive protein (UCRP), is the first identified ubiquitin-like protein containing two ubiquitin-like domains fused in tandem. The active form of ISG15 is conjugated to target proteins via the C-terminal glycine residue through an isopeptide bond in a manner similar to ubiquitin. The biological role of ISG15 is strongly associated with the modulation of cell immune function, and there is mounting evidence suggesting that many viral pathogens evade the host innate immune response by interfering with ISG15 conjugation to both host and viral proteins in a variety of ways. Here we report nearly complete backbone 1HN, 15N, 13CO, and 13Ca, as well as side chain 13Cb, methyl (Ile-d1, Leu, Val), amide (Asn, Gln), and indole NH (Trp) NMR resonance assignments for the 157-residue human ISG15 protein. These resonance assignments provide the basis for future structural and functional solution NMR studies of the biologically important human ISG15 protein.

  3. Easy and unambiguous sequential assignments of intrinsically disordered proteins by correlating the backbone {sup 15}N or {sup 13}C′ chemical shifts of multiple contiguous residues in highly resolved 3D spectra

    Yoshimura, Yuichi; Kulminskaya, Natalia V.; Mulder, Frans A. A., E-mail: fmulder@chem.au.dk [Aarhus University, Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO) (Denmark)

    2015-02-15

    Sequential resonance assignment strategies are typically based on matching one or two chemical shifts of adjacent residues. However, resonance overlap often leads to ambiguity in resonance assignments in particular for intrinsically disordered proteins. We investigated the potential of establishing connectivity through the three-bond couplings between sequentially adjoining backbone carbonyl carbon nuclei, combined with semi-constant time chemical shift evolution, for resonance assignments of small folded and larger unfolded proteins. Extended sequential connectivity strongly lifts chemical shift degeneracy of the backbone nuclei in disordered proteins. We show here that 3D (H)N(COCO)NH and (HN)CO(CO)NH experiments with relaxation-optimized multiple pulse mixing correlate up to seven adjacent backbone amide nitrogen or carbonyl carbon nuclei, respectively, and connections across proline residues are also obtained straightforwardly. Multiple, recurrent long-range correlations with ultra-high resolution allow backbone {sup 1}H{sup N}, {sup 15}N{sup H}, and {sup 13}C′ resonance assignments to be completed from a single pair of 3D experiments.

  4. (H)N(COCA)NH and HN(COCA)NH experiments for 1H-15N backbone assignments in 13C/15N-labeled proteins

    Bracken, Clay; Palmer, Arthur G. III [Columbia University, Department of Biochemistry and Molecular Biophysics (United States); Cavanagh, John [New York State Department of Health, NMR Structural Biology Facility, Wadsworth Center (United States)

    1997-01-15

    Triple resonance HN(COCA)NH pulse sequences for correlating 1H(i), 15N(i),1H(i-1), and 15N(i-1) spins that utilize overlapping coherence transfer periods provide increased sensitivity relative to pulse sequences that utilize sequential coherence transfer periods. Although the overlapping sequence elements reduce the overall duration of the pulse sequences, the principal benefit derives from a reduction in the number of 180 deg. pulses. Two versions of the technique are presented: a 3D (H)N(COCA)NH experiment that correlates 15N(i),1H(i-1), and 15N(i-1) spins, and a 3D HN(COCA)NH experiment that correlates 1H(i), 15N(i),1H(i-1), and 15N(i-1) spins by simultaneously encoding the 1H(i) and 15N(i) chemical shifts during the t1 evolution period. The methods are demonstrated on a 13C/15N-enriched sample of the protein ubiquitin and are easily adapted for application to 2H/13C/15N-enriched proteins.

  5. Combining automated peak tracking in SAR by NMR with structure-based backbone assignment from 15N-NOESY

    Jang, Richard

    2012-03-21

    Background: Chemical shift mapping is an important technique in NMR-based drug screening for identifying the atoms of a target protein that potentially bind to a drug molecule upon the molecule\\'s introduction in increasing concentrations. The goal is to obtain a mapping of peaks with known residue assignment from the reference spectrum of the unbound protein to peaks with unknown assignment in the target spectrum of the bound protein. Although a series of perturbed spectra help to trace a path from reference peaks to target peaks, a one-to-one mapping generally is not possible, especially for large proteins, due to errors, such as noise peaks, missing peaks, missing but then reappearing, overlapped, and new peaks not associated with any peaks in the reference. Due to these difficulties, the mapping is typically done manually or semi-automatically, which is not efficient for high-throughput drug screening.Results: We present PeakWalker, a novel peak walking algorithm for fast-exchange systems that models the errors explicitly and performs many-to-one mapping. On the proteins: hBclXL, UbcH5B, and histone H1, it achieves an average accuracy of over 95% with less than 1.5 residues predicted per target peak. Given these mappings as input, we present PeakAssigner, a novel combined structure-based backbone resonance and NOE assignment algorithm that uses just 15N-NOESY, while avoiding TOCSY experiments and 13C-labeling, to resolve the ambiguities for a one-to-one mapping. On the three proteins, it achieves an average accuracy of 94% or better.Conclusions: Our mathematical programming approach for modeling chemical shift mapping as a graph problem, while modeling the errors directly, is potentially a time- and cost-effective first step for high-throughput drug screening based on limited NMR data and homologous 3D structures. 2012 Jang et al.; licensee BioMed Central Ltd.

  6. Backbone dynamics of free barnase and its complex with barstar determined by 15N NMR relaxation study.

    Sahu, S C; Bhuyan, A K; Udgaonkar, J B; Hosur, R V

    2000-10-01

    Backbone dynamics of uniformly 15N-labeled free barnase and its complex with unlabelled barstar have been studied at 40 degrees C, pH 6.6, using 15N relaxation data obtained from proton-detected 2D [1H]-15N NMR spectroscopy. 15N spin-lattice relaxation rate constants (R1), spin-spin relaxation rate constants (R2), and steady-state heteronuclear [1H]-15N NOEs have been measured at a magnetic field strength of 14.1 Tesla for 91 residues of free barnase and for 90 residues out of a total of 106 in the complex (excluding three prolines and the N-terminal residue) backbone amide 15N sites of barnase. The primary relaxation data for both the cases have been analyzed in the framework of the model-free formalism using both isotropic and axially symmetric models of the rotational diffusion tensor. As per the latter, the overall rotational correlation times (tau(m)) are 5.0 and 9.5 ns for the free and complexed barnase, respectively. The average order parameter is found to be 0.80 for free barnase and 0.86 for the complex. However, the changes are not uniform along the backbone and for about 5 residues near the binding interface there is actually a significant decrease in the order parameters on complex formation. These residues are not involved in the actual binding. For the residues where the order parameter increases, the magnitudes vary significantly. It is observed that the complex has much less internal mobility, compared to free barnase. From the changes in the order parameters, the entropic contribution of NH bond vector motion to the free energy of complex formation has been calculated. It is apparent that these motion's cause significant unfavorable contributions and therefore must be compensated by many other favorable contributions to effect tight complex formation. The observed variations in the motion and their different locations with regard to the binding interface may have important implications for remote effects and regulation of the enzyme action. PMID

  7. Backbone dynamics of free barnase and its complex with barstar determined by 15N NMR relaxation study

    Backbone dynamics of uniformly 15N-labeled free barnase and its complex with unlabelled barstar have been studied at 40 deg. C, pH 6.6, using 15N relaxation data obtained from proton-detected 2D {1H}-15N NMR spectroscopy. 15N spin-lattice relaxation rate constants (R1), spin-spin relaxation rate constants (R2), and steady-state heteronuclear {1H}-15N NOEs have been measured at a magnetic field strength of 14.1 Tesla for 91 residues of free barnase and for 90 residues out of a total of 106 in the complex (excluding three prolines and the N-terminal residue) backbone amide 15N sites of barnase. The primary relaxation data for both the cases have been analyzed in the framework of the model-free formalism using both isotropic and axially symmetric models of the rotational diffusion tensor. As per the latter, the overall rotational correlation times (τm) are 5.0 and 9.5 ns for the free and complexed barnase, respectively. The average order parameter is found to be 0.80 for free barnase and 0.86 for the complex. However, the changes are not uniform along the backbone and for about 5 residues near the binding interface there is actually a significant decrease in the order parameters on complex formation. These residues are not involved in the actual binding. For the residues where the order parameter increases, the magnitudes vary significantly. It is observed that the complex has much less internal mobility, compared to free barnase. From the changes in the order parameters, the entropic contribution of NH bond vector motion to the free energy of complex formation has been calculated. It is apparent that these motions cause significant unfavorable contributions and therefore must be compensated by many other favorable contributions to effect tight complex formation. The observed variations in the motion and their different locations with regard to the binding interface may have important implications for remote effects and regulation of the enzyme action

  8. Backbone dynamics of free barnase and its complex with barstar determined by 15N NMR relaxation study

    Sahu, Sarata C. [Tata Institute of Fundamental Research, Department of Chemical Sciences (India); Bhuyan, Abani K.; Udgaonkar, Jayant B. [University of Agricultural Sciences (UAS), National Centre for Biological Sciences, Tata Institute of Fundamental Research (India); Hosur, R.V. [Tata Institute of Fundamental Research, Department of Chemical Sciences (India)

    2000-10-15

    Backbone dynamics of uniformly {sup 15}N-labeled free barnase and its complex with unlabelled barstar have been studied at 40 deg. C, pH 6.6, using {sup 15}N relaxation data obtained from proton-detected 2D {l_brace}{sup 1}H{r_brace}-{sup 15}N NMR spectroscopy. {sup 15}N spin-lattice relaxation rate constants (R{sub 1}), spin-spin relaxation rate constants (R{sub 2}), and steady-state heteronuclear {l_brace}{sup 1}H{r_brace}-{sup 15}N NOEs have been measured at a magnetic field strength of 14.1 Tesla for 91 residues of free barnase and for 90 residues out of a total of 106 in the complex (excluding three prolines and the N-terminal residue) backbone amide {sup 15}N sites of barnase. The primary relaxation data for both the cases have been analyzed in the framework of the model-free formalism using both isotropic and axially symmetric models of the rotational diffusion tensor. As per the latter, the overall rotational correlation times ({tau}{sub m}) are 5.0 and 9.5 ns for the free and complexed barnase, respectively. The average order parameter is found to be 0.80 for free barnase and 0.86 for the complex. However, the changes are not uniform along the backbone and for about 5 residues near the binding interface there is actually a significant decrease in the order parameters on complex formation. These residues are not involved in the actual binding. For the residues where the order parameter increases, the magnitudes vary significantly. It is observed that the complex has much less internal mobility, compared to free barnase. From the changes in the order parameters, the entropic contribution of NH bond vector motion to the free energy of complex formation has been calculated. It is apparent that these motions cause significant unfavorable contributions and therefore must be compensated by many other favorable contributions to effect tight complex formation. The observed variations in the motion and their different locations with regard to the binding interface

  9. Effects of ion binding on the backbone dynamics of calbindin D9k determined by 15N NMR relaxation.

    Akke, M; Skelton, N J; Kördel, J; Palmer, A G; Chazin, W J

    1993-09-21

    The backbone dynamics of apo- and (Cd2+)1-calbindin D9k have been characterized by 15N nuclear magnetic resonance spectroscopy. Spin-lattice and spin-spin relaxation rate constants and steady-state [1H]-15N nuclear Overhauser effects were measured at a magnetic field strength of 11.74 T by two-dimensional, proton-detected heteronuclear NMR experiments using 15N-enriched samples. The relaxation parameters were analyzed using a model-free formalism that characterizes the dynamics of the N-H bond vectors in terms of generalized order parameters and effective correlation times. The data for the apo and (Cd2+)1 states were compared to those for the (Ca2+)2 state [Kördel, J., Skelton, N. J., Akke, M., Palmer, A. G., & Chazin, W. J. (1992) Biochemistry 31, 4856-4866] to ascertain the effects on ion ligation on the backbone dynamics of calbindin D9k. The two binding loops respond differently to ligation by metal ions: high-frequency (10(9)-10(12) s-1) fluctuations of the N-terminal ion-binding loop are not affected by ion binding, whereas residues G57, D58, G59, and E60 in the C-terminal ion-binding loop have significantly lower order parameters in the apo state than in the metal-bound states. The dynamical responses of the four helices to binding of ions are much smaller than that for the C-terminal binding loop, with the strongest effect on helix III, which is located between the linker loop and binding site II. Significant fluctuations on slower time scales also were detected in the unoccupied N-terminal ion-binding loop of the apo and (Cd2+)1 states; the apparent rates were greater for the (Cd2+)1 state. These results on the dynamical response to ion binding in calbindin D9k provide insights into the molecular details of the binding process and qualitative evidence for entropic contributions to the cooperative phenomenon of calcium binding for the pathway in which the ion binds first in the C-terminal site. PMID:8373781

  10. Backbone and sidechain 1H, 15N and 13C assignments of Tyrosine Phosphatase related to Biofilm formation A (TpbA) of Pseudomonas aeruginosa

    Koveal, Dorothy; Jayasundera, Thusitha B.; Wood, Thomas K.; Peti, Wolfgang; Page, Rebecca

    2012-01-01

    The backbone and side chain resonance assignments of the Tyrosine Phosphatase related to Biofilm formation A (TpbA) of Pseudomonas aeruginosa have been determined based on triple-resonance experiments using uniformly [13C,15N]-labeled protein. This assignment is the first step towards the determination of the 3-dimensional structure of TpbA.

  11. Predicting 15N chemical shifts in proteins using the preceding residue-specific individual shielding surfaces from φ, ψi-1, and χ1torsion angles

    Empirical shielding surfaces are most commonly used to predict chemical shifts in proteins from known backbone torsion angles, φ and ψ. However, the prediction of 15N chemical shifts using this technique is significantly poorer, compared to that for the other nuclei such as 1Hα, 13Cα, and 13Cβ. In this study, we investigated the effects from the preceding residue and the side-chain geometry, χ1, on 15N chemical shifts by statistical methods. For an amino acid sequence XY, the 15N chemical shift of Y is expressed as a function of the amino acid types of X and Y, as well as the backbone torsion angles, φ and ψi-1. Accordingly, 380 empirical 'Preceding Residue Specific Individual (PRSI)' 15N chemical shift shielding surfaces, representing all the combinations of X and Y (except for Y=Pro), were built and used to predict 15N chemical shift from φ and ψi-1. We further investigated the χ1 effects, which were found to account for differences in 15N chemical shifts by ∼5 ppm for amino acids Val, Ile, Thr, Phe, His, Tyr, and Trp. Taking the χ1 effects into account, the χ1-calibrated PRSI shielding surfaces (XPRSI) were built and used to predict 15N chemical shifts for these amino acids. We demonstrated that 15N chemical shift predictions are significantly improved by incorporating the preceding residue and χ1 effects. The present PRSI and XPRSI shielding surfaces were extensively compared with three recently published programs, SHIFTX (Neal et al., 2003), SHIFTS (Xu and Case, 2001 and 2002), and PROSHIFT (Meiler, 2003) on a set of ten randomly selected proteins. A set of Java programs using XPRSI shielding surfaces to predict 15N chemical shifts in proteins were developed and are freely available for academic users at http://www.pronmr.com or by sending email to one of the authors Yunjun Wang

  12. Variation of natural 15N abundance (δ15N) in greenhouse tomato and available nitrogen in soil supplied with cow manure or chemical fertilizers

    Cow manure or chemical fertilizers applied to greenhouse-grown tomato changed N contents and natural 15N abundance (δ15N) in tomato plants and the δ15N values of available N in soil. Cow manure increased and chemical fertilizers decreased the δ15N values of tomato plants. In the early periods of tomato culture with cow manure, the δ15N values of nitrate nitrogen of soil were higher than those of whole cow manure N, and, thereafter, dropped to δ15N values between those of soil and cow manure. Application of chemical fertilizers to soil immediately raised the δ15N values of ammonium nitrogen in soil but they dropped quickly to δ15N values between those of soil and fertilizers. On the estimation of the soil-derived N, manure-derived N and fertilizer-derived N in tomato plants based on the δ15N values of sources, much caution should be paid concerning the isotopic variation caused by N sources and isotopic fractionation during N transformation in soil. (author)

  13. Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology

    Chemical shifts of nuclei in or attached to a protein backbone are exquisitely sensitive to their local environment. A computer program, SPARTA, is described that uses this correlation with local structure to predict protein backbone chemical shifts, given an input three-dimensional structure, by searching a newly generated database for triplets of adjacent residues that provide the best match in φ/ψ/χ1 torsion angles and sequence similarity to the query triplet of interest. The database contains 15N, 1HN, 1Hα, 13Cα, 13Cβ and 13C' chemical shifts for 200 proteins for which a high resolution X-ray (≤2.4 A) structure is available. The relative importance of the weighting factors for the φ/ψ/χ1 angles and sequence similarity was optimized empirically. The weighted, average secondary shifts of the central residues in the 20 best-matching triplets, after inclusion of nearest neighbor, ring current, and hydrogen bonding effects, are used to predict chemical shifts for the protein of known structure. Validation shows good agreement between the SPARTA-predicted and experimental shifts, with standard deviations of 2.52, 0.51, 0.27, 0.98, 1.07 and 1.08 ppm for 15N, 1HN, 1Hα, 13Cα, 13Cβ and 13C', respectively, including outliers

  14. CO{sub H}(N)CACB experiments for assigning backbone resonances in {sup 13}C/{sup 15}N-labeled proteins

    Astrof, Nathan; Bracken, Clay; Cavanagh, John; Palmer, Arthur G

    1998-05-15

    A triple resonance NMR experiment, denoted CO{sub H}(N)CACB, correlates{sup 1}H{sup N} and {sup 13}CO spins with the{sup 13}C{sup {alpha}} and{sup 13}C{sup {beta}} spins of adjacent amino acids. The pulse sequence is an 'out-and-back' design that starts with{sup 1}H{sup N} magnetization and transfers coherence via the {sup 15}N spin simultaneously to the {sup 13}CO and{sup 13}C{sup {alpha}} spins, followed by transfer to the{sup 13}C{sup {beta}} spin. Two versions of the sequence are presented: one in which the {sup 13}CO spins are frequency labeled during an incremented t{sub 1} evolution period prior to transfer of magnetization from the {sup 13}C{sup {alpha}} to the{sup 13}C{sup {beta}} resonances, and one in which the{sup 13}CO spins are frequency labeled in a constant-time manner during the coherence transfer to and from the{sup 13}C{sup {beta}} resonances. Because {sup 13}COand {sup 15}N chemical shifts are largely uncorrelated, the technique will be especially useful when degeneracy in the{sup 1}H{sup N}-{sup 15}N chemical shifts hinders resonance assignment. The CO{sub H}(N)CACB experiment is demonstrated using uniformly {sup 13}C/{sup 15}N-labeled ubiquitin.

  15. Backbone dynamics of a biologically active human FGF-1 monomer, complexed to a hexasaccharide heparin-analogue, by {sup 15}N NMR relaxation methods

    Canales-Mayordomo, Angeles; Fayos, Rosa [Centro de Investigaciones Biologicas, CSIC, Departamento de Estructura y Funcion de Proteinas (Spain); Angulo, Jesus; Ojeda, Rafael [Instituto de Investigaciones Quimicas, CSIC, Grupo de Carbohidratos (Spain); Martin-Pastor, Manuel [Unidad de RM y Unidad de RMN de Biomoleculas Asociada al CSIC, Laboratorio de Estructura e Estructura de Biomoleculas Jose Carracido (Spain); Nieto, Pedro M.; Martin-Lomas, Manuel [Instituto de Investigaciones Quimicas, CSIC, Grupo de Carbohidratos (Spain); Lozano, Rosa; Gimenez-Gallego, Guillermo; Jimenez-Barbero, Jesus [Centro de Investigaciones Biologicas, CSIC, Departamento de Estructura y Funcion de Proteinas (Spain)], E-mail: jjbarbero@cib.csic.es

    2006-08-15

    The binding site and backbone dynamics of a bioactive complex formed by the acidic fibroblast growth factor (FGF-1) and a specifically designed heparin hexasaccharide has been investigated by HSQC and relaxation NMR methods. The comparison of the relaxation data for the free and bound states has allowed showing that the complex is monomeric, and still induces mutagenesis, and that the protein backbone presents reduced motion in different timescale in its bound state, except in certain points that are involved in the interaction with the fibroblast growth factor receptor (FGFR)

  16. Qualitative Study of Substituent Effects on NMR 15N and 17O Chemical Shifts

    Contreras, Rubén H.; Llorente, Tomás; Pagola, Gabriel I.; Bustamante, Manuel G.; Pasqualini, Enrique E.; Melo, Juan I.; Tormena, Cláudio F.

    2009-08-01

    A qualitative approach to analyze the electronic origin of substituent effects on the paramagnetic part of chemical shifts is described and applied to few model systems, where its potentiality can be appreciated. The formulation of this approach is based on the following grounds. The influence of different inter- or intramolecular interactions on a second-order property can be qualitatively predicted if it can be known how they affect the main virtual excitations entering into that second-order property. A set of consistent approximations are introduced in order to analyze the behavior of occupied and virtual orbitals that define some experimental trends of magnetic shielding constants. This approach is applied first to study the electronic origin of methyl-β substituent effects on both 15N and 17O chemical shifts, and afterward it is applied to a couple of examples of long-range substituent effects originated in charge transfer interactions such as the conjugative effect in aromatic compounds and σ-hyperconjugative interactions in saturated multicyclic compounds.

  17. Qualitative study of substituent effects on NMR (15)N and (17)O chemical shifts.

    Contreras, Rubén H; Llorente, Tomás; Pagola, Gabriel I; Bustamante, Manuel G; Pasqualini, Enrique E; Melo, Juan I; Tormena, Cláudio F

    2009-09-10

    A qualitative approach to analyze the electronic origin of substituent effects on the paramagnetic part of chemical shifts is described and applied to few model systems, where its potentiality can be appreciated. The formulation of this approach is based on the following grounds. The influence of different inter- or intramolecular interactions on a second-order property can be qualitatively predicted if it can be known how they affect the main virtual excitations entering into that second-order property. A set of consistent approximations are introduced in order to analyze the behavior of occupied and virtual orbitals that define some experimental trends of magnetic shielding constants. This approach is applied first to study the electronic origin of methyl-beta substituent effects on both (15)N and (17)O chemical shifts, and afterward it is applied to a couple of examples of long-range substituent effects originated in charge transfer interactions such as the conjugative effect in aromatic compounds and sigma-hyperconjugative interactions in saturated multicyclic compounds. PMID:19685922

  18. Detection of closed influenza virus hemagglutinin fusion peptide structures in membranes by backbone {sup 13}CO-{sup 15}N rotational-echo double-resonance solid-state NMR

    Ghosh, Ujjayini; Xie Li; Weliky, David P., E-mail: weliky@chemistry.msu.edu [Michigan State University, Department of Chemistry (United States)

    2013-02-15

    The influenza virus fusion peptide is the N-terminal {approx}20 residues of the HA2 subunit of the hemagglutinin protein and this peptide plays a key role in the fusion of the viral and endosomal membranes during initial infection of a cell. The fusion peptide adopts N-helix/turn/C-helix structure in both detergent and membranes with reports of both open and closed interhelical topologies. In the present study, backbone {sup 13}CO-{sup 15}N REDOR solid-state NMR was applied to the membrane-associated fusion peptide to detect the distribution of interhelical distances. The data clearly showed a large fraction of closed and semi-closed topologies and were best-fitted to a mixture of two structures that do not exchange. One of the earlier open structural models may have incorrect G13 dihedral angles derived from TALOS analysis of experimentally correct {sup 13}C shifts.

  19. (1)H, (13)C, and (15)N backbone resonance assignments of the full-length 40 kDa S. acidocaldarius Y-family DNA polymerase, dinB homolog.

    Moro, Sean L; Cocco, Melanie J

    2015-10-01

    The dinB homolog (Dbh) is a member of the Y-family of translesion DNA polymerases, which are specialized to accurately replicate DNA across from a wide variety of lesions in living cells. Lesioned bases block the progression of high-fidelity polymerases and cause detrimental replication fork stalling; Y-family polymerases can bypass these lesions. The active site of the translesion synthesis polymerase is more open than that of a replicative polymerase; consequently Dbh polymerizes with low fidelity. Bypass polymerases also have low processivity. Short extension past the lesion allows the high-fidelity polymerase to switch back onto the site of replication. Dbh and the other Y-family polymerases have been used as structural models to investigate the mechanisms of DNA polymerization and lesion bypass. Many high-resolution crystal structures of Y-family polymerases have been reported. NMR dynamics studies can complement these structures by providing a measure of protein motions. Here we report the (15)N, (1)H, and (13)C backbone resonance assignments at two temperatures (35 and 50 °C) for Sulfolobus acidocaldarius Dbh polymerase. Backbone resonance assignments have been obtained for 86 % of the residues. The polymerase active site is assigned as well as the majority of residues in each of the four domains. PMID:26154586

  20. Separation of 15N by chemical exchange in NO, NO2 - HNO3 system under pressure

    The basic isotopic exchange reaction is responsible for the separation of 15N in the Nitrox system that between gaseous nitrogen oxides and aqueous nitric acid with a single stage separation factor α = 1.055 for 10M nitric acid, at 25 deg C and atmospheric pressure takes place. In order to know what happens in 15N separation at higher pressure, when the isotopic transport between two phases is improved, a stainless steel laboratory experimental plant with a 1000 mm long x 18 mm i.d. column, packed with triangular wire springs 1.8 x 1.8 x 0.2 mm2, was utilised. At 1.5 atm (absolute), and 2.36 ml x cm-2 x min-1 flow rate HETP was 7% smaller than at atmospheric pressure and 1.5 times smaller flow rate. HETP at 3.14 ml x cm-2 x min-1 flow rate and 1.8 atm is practically equal with that obtained at atmospheric pressure and 2 times smaller flow rate. The operation of the 15N separation plant at 1.8 atm (absolute), instead of atmospheric pressure, will permit doubling of the 10M nitric acid flow rate and of 15N production of the given column. (author)

  1. Inferential protein structure determination and refinement using fast, electronic structure based backbone amide chemical shift predictions

    Christensen, Anders S

    2015-01-01

    This report covers the development of a new, fast method for calculating the backbone amide proton chemical shifts in proteins. Through quantum chemical calculations, structure-based forudsiglese the chemical shift for amidprotonen in protein has been parameterized. The parameters are then implemented in a computer program called Padawan. The program has since been implemented in protein folding program Phaistos, wherein the method andvendes to de novo folding of the protein structures and to refine the existing protein structures.

  2. Automated prediction of 15N, 13Cα, 13Cβ and 13C' chemical shifts in proteins using a density functional database

    A database of peptide chemical shifts, computed at the density functional level, has been used to develop an algorithm for prediction of 15N and 13C shifts in proteins from their structure; the method is incorporated into a program called SHIFTS (version 4.0). The database was built from the calculated chemical shift patterns of 1335 peptides whose backbone torsion angles are limited to areas of the Ramachandran map around helical and sheet configurations. For each tripeptide in these regions of regular secondary structure (which constitute about 40% of residues in globular proteins) SHIFTS also consults the database for information about sidechain torsion angle effects for the residue of interest and for the preceding residue, and estimates hydrogen bonding effects through an empirical formula that is also based on density functional calculations on peptides. The program optionally searches for alternate side-chain torsion angles that could significantly improve agreement between calculated and observed shifts. The application of the program on 20 proteins shows good consistency with experimental data, with correlation coefficients of 0.92, 0.98, 0.99 and 0.90 and r.m.s. deviations of 1.94, 0.97, 1.05, and 1.08 ppm for 15N, 13Cα, 13Cβ and 13C', respectively. Reference shifts fit to protein data are in good agreement with 'random-coil' values derived from experimental measurements on peptides. This prediction algorithm should be helpful in NMR assignment, crystal and solution structure comparison, and structure refinement

  3. Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks

    A new program, TALOS-N, is introduced for predicting protein backbone torsion angles from NMR chemical shifts. The program relies far more extensively on the use of trained artificial neural networks than its predecessor, TALOS+. Validation on an independent set of proteins indicates that backbone torsion angles can be predicted for a larger, ≥90 % fraction of the residues, with an error rate smaller than ca 3.5 %, using an acceptance criterion that is nearly two-fold tighter than that used previously, and a root mean square difference between predicted and crystallographically observed (φ, ψ) torsion angles of ca 12º. TALOS-N also reports sidechain χ1 rotameric states for about 50 % of the residues, and a consistency with reference structures of 89 %. The program includes a neural network trained to identify secondary structure from residue sequence and chemical shifts

  4. Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks

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

    2013-07-15

    A new program, TALOS-N, is introduced for predicting protein backbone torsion angles from NMR chemical shifts. The program relies far more extensively on the use of trained artificial neural networks than its predecessor, TALOS+. Validation on an independent set of proteins indicates that backbone torsion angles can be predicted for a larger, {>=}90 % fraction of the residues, with an error rate smaller than ca 3.5 %, using an acceptance criterion that is nearly two-fold tighter than that used previously, and a root mean square difference between predicted and crystallographically observed ({phi}, {psi}) torsion angles of ca 12 Masculine-Ordinal-Indicator . TALOS-N also reports sidechain {chi}{sup 1} rotameric states for about 50 % of the residues, and a consistency with reference structures of 89 %. The program includes a neural network trained to identify secondary structure from residue sequence and chemical shifts.

  5. Measurement of {sup 15}N relaxation in deuterated amide groups in proteins using direct nitrogen detection

    Vasos, Paul R.; Hall, Jennifer B. [University of Maryland, Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization (United States); Kuemmerle, Rainer [Bruker Biospin AG, NMR Division (Switzerland); Fushman, David [University of Maryland, Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization (United States)], E-mail: fushman@umd.edu

    2006-09-15

    {sup 15}N chemical shielding tensors contain useful structural information, and their knowledge is essential for accurate analysis of protein backbone dynamics. The anisotropic component (CSA) of {sup 15}N chemical shielding can be obtained from {sup 15}N relaxation measurements in solution. However, the predominant contribution to nitrogen relaxation from {sup 15}N-{sup 1}H dipolar coupling in amide groups limits the sensitivity of these measurements to the actual CSA values. Here we present nitrogen-detected NMR experiments for measuring {sup 15}N relaxation in deuterated amide groups in proteins, where the dipolar contribution to {sup 15}N relaxation is significantly reduced by the deuteration. Under these conditions nitrogen spin relaxation becomes a sensitive probe for variations in {sup 15}N chemical shielding tensors. Using the nitrogen direct-detection experiments we measured the rates of longitudinal and transverse {sup 15}N relaxation for backbone amides in protein G in D{sub 2}O at 11.7 T. The measured relaxation rates are validated by comparing the overall rotational diffusion tensor obtained from these data with that from the conventional {sup 15}N relaxation measurements in H{sub 2}O. This analysis revealed a 17-24{sup o} angle between the NH-bond and the unique axis of the {sup 15}N chemical shielding tensor.

  6. Measurement of 15N relaxation in deuterated amide groups in proteins using direct nitrogen detection

    15N chemical shielding tensors contain useful structural information, and their knowledge is essential for accurate analysis of protein backbone dynamics. The anisotropic component (CSA) of 15N chemical shielding can be obtained from 15N relaxation measurements in solution. However, the predominant contribution to nitrogen relaxation from 15N-1H dipolar coupling in amide groups limits the sensitivity of these measurements to the actual CSA values. Here we present nitrogen-detected NMR experiments for measuring 15N relaxation in deuterated amide groups in proteins, where the dipolar contribution to 15N relaxation is significantly reduced by the deuteration. Under these conditions nitrogen spin relaxation becomes a sensitive probe for variations in 15N chemical shielding tensors. Using the nitrogen direct-detection experiments we measured the rates of longitudinal and transverse 15N relaxation for backbone amides in protein G in D2O at 11.7 T. The measured relaxation rates are validated by comparing the overall rotational diffusion tensor obtained from these data with that from the conventional 15N relaxation measurements in H2O. This analysis revealed a 17-24o angle between the NH-bond and the unique axis of the 15N chemical shielding tensor

  7. 1H, 13C and 13N chemical shifts and 1H-15N and 13C-15N heteronuclear spin-spin coupling constants n the NMR spectra of 5-substituted furfural oximes

    The 1H, 13C, and 15N NMR spectra of 15N-enriched 5-substituted furfural oximes were investigated. It was shown that the chemical shifts of the ring atoms and the oxime group correlate satisfactorily with the F and R substituent constants, whereas their sensitivity to the effect of the substituents is lower than in monosubstituted furan derivatives. The constants of spin-spin coupling between the ring protons and the oxime group were determined. An analysis of the 1H-1H spin-spin coupling constants (SSCC) on the basis of their stereospecificity indicates that the E isomers have primarily an s-trans conformation in polar dimethyl sulfoxide, whereas the Z isomers, on the other hand, have an s-cis conformation. The signs of the direct and geminal 13C-15N SSCC were determined for 5-trimethylsilylfurfural oxime

  8. Quantum chemical benchmark study on 46 RNA backbone families using a dinucleotide unit.

    Kruse, Holger; Mladek, Arnost; Gkionis, Konstantinos; Hansen, Andreas; Grimme, Stefan; Sponer, Jiri

    2015-10-13

    We have created a benchmark set of quantum chemical structure-energy data denoted as UpU46, which consists of 46 uracil dinucleotides (UpU), representing all known 46 RNA backbone conformational families. Penalty-function-based restrained optimizations with COSMO TPSS-D3/def2-TZVP ensure a balance between keeping the target conformation and geometry relaxation. The backbone geometries are close to the clustering-means of their respective RNA bioinformatics family classification. High-level wave function methods (DLPNO-CCSD(T) as reference) and a wide-range of dispersion-corrected or inclusive DFT methods (DFT-D3, VV10, LC-BOP-LRD, M06-2X, M11, and more) are used to evaluate the conformational energies. The results are compared to the Amber RNA bsc0χOL3 force field. Most dispersion-corrected DFT methods surpass the Amber force field significantly in accuracy and yield mean absolute deviations (MADs) for relative conformational energies of ∼0.4-0.6 kcal/mol. Double-hybrid density functionals represent the most accurate class of density functionals. Low-cost quantum chemical methods such as PM6-D3H+, HF-3c, DFTB3-D3, as well as small basis set calculations corrected for basis set superposition errors (BSSEs) by the gCP procedure are also tested. Unfortunately, the presently available low-cost methods are struggling to describe the UpU conformational energies with satisfactory accuracy. The UpU46 benchmark is an ideal test for benchmarking and development of fast methods to describe nucleic acids, including force fields. PMID:26574283

  9. Quantum Chemical Benchmark Study on 46 RNA Backbone Families Using a Dinucleotide Unit

    Kruse, H.; Mládek, Arnošt; Gkionis, Konstantinos; Hansen, A.; Grimme, S.; Šponer, Jiří

    2015-01-01

    Roč. 11, č. 10 (2015), s. 4972-4991. ISSN 1549-9618 R&D Projects: GA ČR(CZ) GBP305/12/G034 Institutional support: RVO:68081707 Keywords : MOLECULAR-DYNAMICS SIMULATIONS * DENSITY-FUNCTIONAL THEORY * SUGAR-PHOSPHATE BACKBONE Subject RIV: BO - Biophysics Impact factor: 5.498, year: 2014

  10. (1)H, (13)C, and (15)N chemical shift assignments of cyanobacteriochrome NpR6012g4 in the green-absorbing photoproduct state.

    Lim, Sunghyuk; Yu, Qinhong; Rockwell, Nathan C; Martin, Shelley S; Lagarias, J Clark; Ames, James B

    2016-04-01

    Cyanobacteriochromes (CBCRs) are cyanobacterial photosensory proteins with a tetrapyrrole (bilin) chromophore that belong to the phytochrome superfamily. Like phytochromes, CBCRs photoconvert between two photostates with distinct spectral properties. NpR6012g4 from Nostoc punctiforme is a model system for widespread CBCRs with conserved red/green photocycles. Atomic-level structural information for the photoproduct state in this subfamily is not known. Here, we report NMR backbone chemical shift assignments of the light-activated state of NpR6012g4 (BMRB no. 26577) as a first step toward determining its atomic resolution structure. PMID:26537963

  11. Quantification of protein backbone hydrogen-deuterium exchange rates by solid state NMR spectroscopy

    Lopez del Amo, Juan-Miguel; Fink, Uwe; Reif, Bernd, E-mail: reif@tum.d [Leibniz-Institut fuer Molekulare Pharmakologie (FMP) (Germany)

    2010-12-15

    We present the quantification of backbone amide hydrogen-deuterium exchange rates (HDX) for immobilized proteins. The experiments make use of the deuterium isotope effect on the amide nitrogen chemical shift, as well as on proton dilution by deuteration. We find that backbone amides in the microcrystalline {alpha}-spectrin SH3 domain exchange rather slowly with the solvent (with exchange rates negligible within the individual {sup 15}N-T{sub 1} timescales). We observed chemical exchange for 6 residues with HDX exchange rates in the range from 0.2 to 5 s{sup -1}. Backbone amide {sup 15}N longitudinal relaxation times that we determined previously are not significantly affected for most residues, yielding no systematic artifacts upon quantification of backbone dynamics (Chevelkov et al. 2008b). Significant exchange was observed for the backbone amides of R21, S36 and K60, as well as for the sidechain amides of N38, N35 and for W41{epsilon}. These residues could not be fit in our previous motional analysis, demonstrating that amide proton chemical exchange needs to be considered in the analysis of protein dynamics in the solid-state, in case D{sub 2}O is employed as a solvent for sample preparation. Due to the intrinsically long {sup 15}N relaxation times in the solid-state, the approach proposed here can expand the range of accessible HDX rates in the intermediate regime that is not accessible so far with exchange quench and MEXICO type experiments.

  12. Backbone and stereospecific (13)C methyl Ile (δ1), Leu and Val side-chain chemical shift assignments of Crc.

    Sharma, Rakhi; Sahu, Bhubanananda; Ray, Malay K; Deshmukh, Mandar V

    2015-04-01

    Carbon catabolite repression (CCR) allows bacteria to selectively assimilate a preferred compound among a mixture of several potential carbon sources, thus boosting growth and economizing the cost of adaptability to variable nutrients in the environment. The RNA-binding catabolite repression control (Crc) protein acts as a global post-transcriptional regulator of CCR in Pseudomonas species. Crc triggers repression by inhibiting the expression of genes involved in transport and catabolism of non-preferred substrates, thus indirectly favoring assimilation of preferred one. We report here a nearly complete backbone and stereospecific (13)C methyl side-chain chemical shift assignments of Ile (δ1), Leu and Val of Crc (~ 31 kDa) from Pseudomonas syringae Lz4W. PMID:24496608

  13. Pseudo 5D HN(C)N Experiment to Facilitate the Assignment of Backbone Resonances in Proteins Exhibiting High Backbone Shift Degeneracy

    Kumar, Dinesh; Shukla, Vaibhav Kumar; Pandey, Himanshu; Arora, Ashish; Guleria, Anupam

    2014-01-01

    Assignment of protein backbone resonances is most routinely carried out using triple resonance three dimensional NMR experiments involving amide 1H and 15N resonances. However for intrinsically unstructured proteins, alpha-helical proteins or proteins containing several disordered fragments, the assignment becomes problematic because of high degree of backbone shift degeneracy. In this backdrop, a novel reduced dimensionality (RD) experiment -(5,3)D-hNCO-CANH- is presented to facilitate (and/or to validate) the sequential backbone resonance assignment in such proteins. The proposed 3D NMR experiment makes use of the modulated amide 15N chemical shifts (resulting from the joint sampling along both its indirect dimensions) to resolve the ambiguity involved in connecting the neighboring amide resonances (i.e. HiNi and Hi-1Ni-1) for overlapping amide NH peaks. The experiment -encoding 5D spectral information- leads to a conventional 3D spectrum with significantly reduced spectral crowding and complexity. The impr...

  14. Pressure dependence of backbone chemical shifts in the model peptides Ac-Gly-Gly-Xxx-Ala-NH2.

    Erlach, Markus Beck; Koehler, Joerg; Crusca, Edson; Kremer, Werner; Munte, Claudia E; Kalbitzer, Hans Robert

    2016-06-01

    For a better understanding of nuclear magnetic resonance (NMR) detected pressure responses of folded as well as unstructured proteins the availability of data from well-defined model systems are indispensable. In this work we report the pressure dependence of chemical shifts of the backbone atoms (1)H(α), (13)C(α) and (13)C' in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH2 (Xxx one of the 20 canonical amino acids). Contrary to expectation the chemical shifts of these nuclei have a nonlinear dependence on pressure in the range from 0.1 to 200 MPa. The polynomial pressure coefficients B 1 and B 2 are dependent on the type of amino acid studied. The coefficients of a given nucleus show significant linear correlations suggesting that the NMR observable pressure effects in the different amino acids have at least partly the same physical cause. In line with this observation the magnitude of the second order coefficients of nuclei being direct neighbors in the chemical structure are also weakly correlated. PMID:27335085

  15. Combined solid state and solution NMR studies of {alpha},{epsilon}-{sup 15}N labeled bovine rhodopsin

    Werner, Karla; Lehner, Ines [Johann Wolfgang Goethe-Universitaet Frankfurt, Center for Biomolecular Magnetic Resonance (Germany); Dhiman, Harpreet Kaur [University of Pittsburgh School of Medicine, Department of Structural Biology (United States); Richter, Christian; Glaubitz, Clemens; Schwalbe, Harald, E-mail: schwalbe@nmr.uni-frankfurt.de; Klein-Seetharaman, Judith [Johann Wolfgang Goethe-Universitaet Frankfurt, Center for Biomolecular Magnetic Resonance (Germany); Khorana, H. Gobind [Massachusetts Institute of Technology, Departments of Biology and Chemistry (United States)], E-mail: khorana@mit.edu

    2007-04-15

    Rhodopsin is the visual pigment of the vertebrate rod photoreceptor cell and is the only member of the G protein coupled receptor family for which a crystal structure is available. Towards the study of dynamics in rhodopsin, we report NMR-spectroscopic investigations of {alpha},{epsilon}-{sup 15}N-tryptophan labeled rhodopsin in detergent micelles and reconstituted in phospholipids. Using a combination of solid state {sup 13}C,{sup 15}N-REDOR and HETCOR experiments of all possible {sup 13}C'{sub i-1} carbonyl/{sup 15}N{sub i}-tryptophan isotope labeled amide pairs, and H/D exchange {sup 1}H,{sup 15}N-HSQC experiments conducted in solution, we assigned chemical shifts to all five rhodopsin tryptophan backbone {sup 15}N nuclei and partially to their bound protons. {sup 1}H,{sup 15}N chemical shift assignment was achieved for indole side chains of Trp35{sup 1.30} and Trp175{sup 4.65}. {sup 15}N chemical shifts were found to be similar when comparing those obtained in the native like reconstituted lipid environment and those obtained in detergent micelles for all tryptophans except Trp175{sup 4.65} at the membrane interface. The results suggest that the integrated solution and solid state NMR approach presented provides highly complementary information in the study of structure and dynamics of large membrane proteins like rhodopsin.

  16. Pseudo 5D HN(C)N experiment to facilitate the assignment of backbone resonances in proteins exhibiting high backbone shift degeneracy

    Kumar, Dinesh, E-mail: dineshcbmr@gmail.com [Centre of Biomedical Research (CBMR), SGPGIMS Campus, Raibareli Road, Lucknow 226014 (India); Raikwal, Nisha [Centre of Biomedical Research (CBMR), SGPGIMS Campus, Raibareli Road, Lucknow 226014 (India); Shukla, Vaibhav Kumar; Pandey, Himanshu; Arora, Ashish [Molecular and Structural Biology Division, CSIR, Central Drug Research Institute, Lucknow 226031 (India); Guleria, Anupam, E-mail: anuguleriaphy@gmail.com [Centre of Biomedical Research (CBMR), SGPGIMS Campus, Raibareli Road, Lucknow 226014 (India)

    2014-09-30

    Graphical abstract: - Highlights: • A reduced dimensionality experiment – referred as pseudo 5D HN(C)N- is presented. • Encodes highly resolved 5D spectral information in a 3D spectrum. • Superior in terms of peak dispersion. • Facilitates assignment of crowded HSQC spectra of moderately sized proteins. • Modulated {sup 15}N chemical shifts are used to break the amide shift degeneracy. - Abstract: Assignment of protein backbone resonances is most routinely carried out using triple resonance three-dimensional NMR experiments involving amide {sup 1}H/{sup 15}N resonances. However for intrinsically unstructured proteins, alpha-helical proteins or proteins containing several disordered fragments, the assignment becomes problematic because of high-degree of backbone shift degeneracy. In this backdrop, a novel reduced-dimensionality (RD) experiment –(5, 3)D-hNCO-CANH- is presented to facilitate/validate the sequential backbone resonance assignment in such proteins. The proposed 3D NMR experiment makes use of the modulated amide {sup 15}N chemical shifts (resulting from the joint sampling along both its indirect dimensions) to resolve the ambiguity involved in connecting the neighboring amide resonances (i.e. H{sub i}N{sub i} and H{sub i−1}N{sub i−1}) for overlapping amide-NH peaks. The experiment -in combination with routine triple resonance 3D-NMR experiments involving backbone amide ({sup 1}H/{sup 15}N) and carbon ({sup 13}C{sup α}/{sup 13}C′) chemical shifts- will serve as a powerful complementary tool to achieve the nearly complete assignment of protein backbone resonances in a time efficient manner.

  17. Automated protein backbone assignment using the projection-decomposition approach

    Spectral projection experiments by NMR in conjunction with decomposition analysis have been previously introduced for the backbone assignment of proteins; various pulse sequences as well as the behaviour with low signal-to-noise or chemical shift degeneracy have been illustrated. As a guide for routine applications of this combined tool, we provide here a systematic analysis on different types of proteins using welldefined run-time parameters. As a second result of this study, the backbone assignment module SHABBA was extensively rewritten and improved. Calculations on ubiquitin yielded again fully correct and nearly complete backbone and CHβ assignments. For the 128 residue long azurin, missing assignments mostly affect Hα and Hβ. Among the remaining backbone (plus Cβ) nuclei 97.5% could be assigned with 1.0% differences to a reference. Finally, the new SHABBA algorithm was applied to projections recorded for a yeast histone protein domain at room temperature, where the protein is subject to partial unfolding: this leads to unobservable resonances (about a dozen missing signals in a normal 15N-HSQC) and extensive degeneracy among the resonances. From the clearly observable residues, 97.5% of the backbone and CHβresonances could be assigned, of which only 0.8 % showed differences to published shifts. An additional study on the protein MMP20, which exhibits spectral difficulties to an even larger extent, explores the limitations of the approach.

  18. (1)H, (15)N and (13)C chemical shift assignment of the Gram-positive conjugative transfer protein TraHpIP501.

    Fercher, Christian; Keller, Walter; Zangger, Klaus; Helge Meyer, N

    2016-04-01

    Conjugative transfer of DNA represents the most important transmission pathway in terms of antibiotic resistance and virulence gene dissemination among bacteria. TraH is a putative transfer protein of the type IV secretion system (T4SS) encoded by the Gram-positive (G+) conjugative plasmid pIP501. This molecular machine involves a multi-protein core complex spanning the bacterial envelope thereby serving as a macromolecular secretion channel. Here, we report the near complete (1)H, (13)C and (15)N resonance assignment of a soluble TraH variant comprising the C-terminal domain. PMID:26559076

  19. Backbone and sidechain 1H, 13C and 15N resonance assignments of the human brain-type fatty acid binding protein (FABP7) in its apo form and the holo forms binding to DHA, oleic acid, linoleic acid and elaidic acid

    Oeemig, Jesper S; Jørgensen, Mathilde L; Hansen, Mikka S;

    2009-01-01

    In this manuscript, we present the backbone and side chain assignments of human brain-type fatty acid binding protein, also known as FABP7, in its apo form and in four different holo forms, bound to DHA, oleic acid, linoleic acid and elaidic acid.......In this manuscript, we present the backbone and side chain assignments of human brain-type fatty acid binding protein, also known as FABP7, in its apo form and in four different holo forms, bound to DHA, oleic acid, linoleic acid and elaidic acid....

  20. Evolution of the chemical (NH4) and isotopic (δ15N-NH4) composition of pig manure stored in an experimental deep pit

    during eight months, from November 2001 to July 2002 at atmospheric conditions. Ammonium concentration and its nitrogen isotopic composition were analysed weekly during the first six months and every ten days during the last two months. Ammonium concentration oscillates between 3000 and 4000 ppm, with no progressive decrease in time as it would be expected in a volatilisation process. This is caused by the loss of manure volume due to evaporation (50 % in eight months) which compensates the ammonia volatilisation and keeps the ammonium concentration stable. The nitrogen isotopic composition of the ammonium is controlled by the volatilisation process. During the first ten days, the pig manure has an isotopic composition between +8 and +10 per mille, and after eight months, it raises up to +25 per mille. However, the pig manure is not stored in the deep pits more than six months; consequently, the range of δ15NNH4 values to be considered for pig manure as an input of nitrogen contamination should be from +8 to +15 per mille. Still, this isotopic composition can be higher if manure is stored during the summer time since the higher temperatures may increase the volatilisation rate and raise the ammonium isotopic composition in a shorter period of time. Unlike synthetic fertilisers, which are characterised by a δ15N close to the 0 per mille, the organic fertilisers (pig manure) are enriched in 15N15N from +8 to +15 per mille). Therefore the nitrogen isotopic composition is a valuable tool to evaluate the origin of nitrate agricultural contaminations. As an example, nitrate nitrogen isotopic composition has been used in some areas in Catalonia to confirm that pig manure is the main contributor to the nitrate pollution in groundwaters

  1. Orientation Preferences of Backbone Secondary Amide Functional Groups in Peptide Nucleic Acid Complexes: Quantum Chemical Calculations Reveal an Intrinsic Preference of Cationic D-Amino Acid-Based Chiral PNA Analogues for the P-form

    Topham, Christopher M.; Smith, Jeremy C.

    2006-01-01

    Geometric descriptions of nonideal interresidue hydrogen bonding and backbone-base water bridging in the minor groove are established in terms of polyamide backbone carbonyl group orientation from analyses of residue junction conformers in experimentally determined peptide nucleic acid (PNA) complexes. Two types of interresidue hydrogen bonding are identified in PNA conformers in heteroduplexes with nucleic acids that adopt A-like basepair stacking. Quantum chemical calculations on the bindin...

  2. 15N analysis in nutritional and metabolic research of infancy

    Investigation of protein metabolism in nutritional pediatric research by means of 15N tracer techniques has been relatively seldom used up to now. 15N-labelled compounds for these purposes are not injurious to health. The technique is based on oral or intravenous application of the tracer substances and on 15N analysis of the urine fractions. The subsequent calculation of protein synthesis and breakdown rate, turnover, and the reutilisation of amino acids from protein breakdown as well as the size of the metabolic pool offers detailed information of protein metabolism. Determination of these parameters were performed in infants on breast milk, formula feeding and on chemically defined diet. As an example of utilisation of D-amino acids for protein synthesis the 15N-D-phenylalanine retention of parenteral nutrition was found to be 33% of the applied dosis at an average. An oral 15N-glycine loading test proved to be of value for the prediction of the therapeutic effect of human growth hormone. 15N tracer technique was also tested in utilizing 15N-urea for bacterial protein synthesis of the intestinal flora and by incorporation of 15N from 15N-glycine and 15N-lysine into the jejunal mucosa for measuring the enterocyte regeneration. (author)

  3. Methods of 15N tracer research in biological systems

    The application of the stable isotope 15N is of increasing importance in different scientific disciplines, especially in medicine, agriculture, and the biosciences. The close correlation between the growing interest and improvements of analytical procedures resulted in remarkable advances in the 15N tracer technique. On the basis of the latest results of 15N tracer research in life sciences and agriculture methods of 15N tracer research in biological systems are compiled. The 15N methodology is considered under three headings: Chemical analysis with a description of methods of sample preparation (including different separation and isolation methods for N-containing substances of biological and agricultural origin) and special procedures converting ammonia to molecular nitrogen. Isotopic analysis with a review on the most important methods of isotopic analysis of nitrogen: mass spectrometry (including the GC-MS technique), emission spectrometry, NMR spectroscopy, and other analytical procedures. 15N-tracer techniques with a consideration of the role of the isotope dilution analysis as well as different labelling techniques and the mathematical interpretation of tracer data (modelling, N turnover experiments). In these chapters also sources of errors in chemical and isotopic analysis, the accuracy of the different methods and its importance on tracer experiments are discussed. Procedures for micro scale 15N analysis and aspects of 15N analysis on the level of natural abundance are considered. Furthermore some remarks on isotope effects in 15N tracer experiments are made. (author)

  4. Synthesis of 15N labeled glyphosate

    Amongst the actually commercialized herbicides the Glyphosate is the most used in Brazil. Its efficiency as well as the others herbicides against undesirable weeds is harmed by its final composts left at the environment. Although studies has being carried out to improve the knowledge about the herbicides behavior at the environment its complexity has led them towards innumerous to new significant research work where the use of radiolabeled composts (radiative tracers) are recommended to evaluate their bio-availability in the soil. However is the use, the manipulation and the storage of radiolabeled composts is requires an extra care under chemical safety point of view. The use of non radiolabeled composts is a world tendency especially for field researches. Under this context the presented work describes a method for the synthesis of 15N labeled glyphosate. The 15N-herbicide was undertaken by phosphometilation with the phosphit dialquil and 15N-glycine. The tests where carried out through a micro scale production plant and of equimolars amounts. At these conditions it's was possible to reach approximately a 20% of yield. At the conclusion of a best operational condition its expected to offer another important toll that shall be used in glyphosate behavior at the environment and undesirably weeds. (author)

  5. Testing Backbone.js

    Roemer, Ryan

    2013-01-01

    This book is packed with the step by step tutorial and instructions in recipe format helping you setup test infrastructure and gradually advance your skills to plan, develop, and test your backbone applications.If you are a JavaScript developer looking for recipes to create and implement test support for your backbone application, then this book is ideal for you.

  6. NMR spectroscopic studies of 15N labelled geminally disubstituted cyclotriphosphazenes

    It is demonstrated by means of some selected 15N labelled geminally disubstituted cyclotriphosphazenes, 15N3P3X4Y2 (X = Cl; Y = F, NH2, or SEt), as an example, that the coupling constants 1Jsub(PN) may be of different signs. The absolute value of 1Jsub(PN) is significantly influenced only by those substituents, which are bonded to the phosphorus nucleus directly concerned in the coupling. Also the 15N chemical shifts are only changed by substituents on directly bonded phosphorus atoms. (author)

  7. Orientation Preferences of Backbone Secondary Amide Functional Groups in Peptide Nucleic Acid Complexes: Quantum Chemical Calculations Reveal an Intrinsic Preference of Cationic D-Amino Acid-Based Chiral PNA Analogues for the P-form

    Smith, Jeremy C [ORNL; Topham, Christopher [University of Heidelberg

    2007-01-01

    Geometric descriptions of nonideal interresidue hydrogen bonding and backbone-base water bridging in the minor groove are established in terms of polyamide backbone carbonyl group orientation from analyses of residue junction conformers in experimentally determined peptide nucleic acid (PNA) complexes. Two types of interresidue hydrogen bonding are identified in PNA conformers in heteroduplexes with nucleic acids that adopt A-like base pair stacking. Quantum chemical calculations on the binding of a water molecule to an O2 base atom in glycine-based PNA thymine dimers indicate that junctions modeled with P-form backbone conformations are lower in energy than a dimer comprising the predominant conformation observed in A-like helices. It is further shown in model systems that PNA analogs based on D-lysine are better able to preorganize in a conformation exclusive to P-form helices than is glycine-based PNA. An intrinsic preference for this conformation is also exhibited by positively charged chiral PNA dimers carrying 3-amino-D-alanine or 4-aza-D-leucine residue units that provide for additional rigidity by side-chain hydrogen bonding to the backbone carbonyl oxygen. Structural modifications stabilizing P-form helices may obviate the need for large heterocycles to target DNA pyrimidine bases via PNADNA-PNA triplex formation. Quantum chemical modeling methods are used to propose candidate PNA Hoogsteen strand designs.

  8. Orientation preferences of backbone secondary amide functional groups in peptide nucleic acid complexes: quantum chemical calculations reveal an intrinsic preference of cationic D-amino acid-based chiral PNA analogues for the P-form.

    Topham, Christopher M; Smith, Jeremy C

    2007-02-01

    Geometric descriptions of nonideal interresidue hydrogen bonding and backbone-base water bridging in the minor groove are established in terms of polyamide backbone carbonyl group orientation from analyses of residue junction conformers in experimentally determined peptide nucleic acid (PNA) complexes. Two types of interresidue hydrogen bonding are identified in PNA conformers in heteroduplexes with nucleic acids that adopt A-like basepair stacking. Quantum chemical calculations on the binding of a water molecule to an O2 base atom in glycine-based PNA thymine dimers indicate that junctions modeled with P-form backbone conformations are lower in energy than a dimer comprising the predominant conformation observed in A-like helices. It is further shown in model systems that PNA analogs based on D-lysine are better able to preorganize in a conformation exclusive to P-form helices than is glycine-based PNA. An intrinsic preference for this conformation is also exhibited by positively charged chiral PNA dimers carrying 3-amino-D-alanine or 4-aza-D-leucine residue units that provide for additional rigidity by side-chain hydrogen bonding to the backbone carbonyl oxygen. Structural modifications stabilizing P-form helices may obviate the need for large heterocycles to target DNA pyrimidine bases via PNA.DNA-PNA triplex formation. Quantum chemical modeling methods are used to propose candidate PNA Hoogsteen strand designs. PMID:17071666

  9. Changes in Rhodospirillum rubrum cytochrome c2 and subsequent renaturation: An 15N NMR study

    The 15N-enriched ferrocytochrome c2from Rhodospirillum rubrum was studied by 15N NMR at different solvent pH values. The mobility and chemical shift to the N-terminal glutamic acid (335.4 ppm at pH 5.1) were found to depend on pH. It was least mobile between pH 8 and 9.0, which is explained in terms of pH-dependent conformational changes and formation of salt linkages and/or hydrogen bonds. The resonances of the lysine side chains are centered around 341.7 ppm at low pH and move upfield with pH by about 8.4 ppm with pH/sub a/ values of 10.8. The exchange rates of the εNH protons are lowest near the pK/sub a/ values. The protein is very stable in the pH range between 4.9 and 10.0 but unfolds abruptly at pH 10.5-11. Denaturation was verified by the measurement of several parameters by NMR. The renaturation of the protein demonstrates that the folding begins with reformation of home coordination and establishment of a hydrophobic core, followed by positioning of side chains and peptide backbones linking the nucleation centers. The repositioning processes had time scales of minutes to hours in contrast to the reported values of seconds in some studies

  10. Reduced Dimensionality (4,3)D-hnCOCANH Experiment: An Efficient Backbone Assignment tool for NMR studies of Proteins

    Kumar, Dinesh

    2013-01-01

    Sequence specific resonance assignment and secondary structure determination of proteins form the basis for variety of structural and functional proteomics studies by NMR. In this context, an efficient standalone method for rapid assignment of backbone (1H, 15N, 13Ca and 13C') resonances and secondary structure determination of proteins has been presented here. Compared to currently available strategies used for the purpose, the method employs only a single reduced dimensionality (RD) experiment -(4,3)D-hnCOCANH and exploits the linear combinations of backbone (13Ca and 13C') chemical shifts to achieve a dispersion relatively better compared to those of individual chemical shifts (see the text) for efficient and rapid data analysis. Further, the experiment leads to the spectrum with direct distinction of self (intra-residue) and sequential (inter-residue) carbon correlation peaks; these appear opposite in signs and therefore can easily be discriminated without using an additional complementary experiment. On ...

  11. Synthesis of {sup 15}N labeled glyphosate; Sintese do glifosato enriquecido com {sup 15}N

    Oliveira, Claudineia R. de; Bendassolli, Jose Albertino; Tavares, Glauco Arnold; Rossete, Alexssandra L.R.M.; Tagliassachi, Romulo Barbieri; Prestes, Cleuber Vieira [Centro de Energia Nuclear na Agricultura (CENA), Piracicaba, SP (Brazil). Dept. de Isotopos Estaveis]. E-mail: crolivei@cena.usp.br

    2005-07-01

    Amongst the actually commercialized herbicides the Glyphosate is the most used in Brazil. Its efficiency as well as the others herbicides against undesirable weeds is harmed by its final composts left at the environment. Although studies has being carried out to improve the knowledge about the herbicides behavior at the environment its complexity has led them towards innumerous to new significant research work where the use of radiolabeled composts (radiative tracers) are recommended to evaluate their bio-availability in the soil. However is the use, the manipulation and the storage of radiolabeled composts is requires an extra care under chemical safety point of view. The use of non radiolabeled composts is a world tendency especially for field researches. Under this context the presented work describes a method for the synthesis of {sup 15}N labeled glyphosate. The {sup 15}N-herbicide was undertaken by phosphometilation with the phosphit dialquil and {sup 15}N-glycine. The tests where carried out through a micro scale production plant and of equimolars amounts. At these conditions it's was possible to reach approximately a 20% of yield. At the conclusion of a best operational condition its expected to offer another important toll that shall be used in glyphosate behavior at the environment and undesirably weeds. (author)

  12. Complete assignment of 1H, 13C and 15N chemical shifts for bovine β-lactoglobulin: Secondary structure and topology of the native state is retained in a partially unfolded form

    Although β-lactoglobulin (β-LG) has been studied extensively for more than 50 years, its physical properties in solution are not yet understood fully in terms of its three-dimensional (3D) structure. For example, despite a recent high-resolution crystal structure, it is still not clear why the two common variants of bovine β-LG which differ by just two residues have different aggregation properties during milk processing. We have conducted solution-state NMR studies on a recombinant form of the A variant of β-LG at low pH conditions where the protein is partially unfolded and exists as a monomer rather than a dimer. Using a13 C,15N-labelled sample, expressed in Pichia pastoris, we have employed the standard combination of 3D heteronuclear NMR techniques to obtain near complete assignments of proton, carbon and nitrogen resonances. Using a novel pulse sequence we were able to obtain additional assignments, in particular those of methyl groups in residues preceding proline within the sequence. From chemical shifts and on the basis of inter-residue NOEs, we have inferred the secondary structure and topology of monomeric β-LG A. It includes eight antiparallel β-strands arranged in a barrel, flanked by an α-helix, which is typical of a member of the lipocalin family. A detailed comparison with the crystal structure of the dimeric form (for a mixture of A and B variants) at pH 6.5 reveals a close resemblance in both secondary structure and overall topology. Both forms have a ninth β-strand which, at the higher pH, forms part of the dimer interface. These studies represent the first full NMR assignment of β-LG and will form the basis for a complete characterisation of the solution structure and dynamics of this protein and its variants

  13. Backbone amide linker strategy

    Shelton, Anne Pernille Tofteng; Jensen, Knud Jørgen

    2013-01-01

    In the backbone amide linker (BAL) strategy, the peptide is anchored not at the C-terminus but through a backbone amide, which leaves the C-terminal available for various modifications. This is thus a very general strategy for the introduction of C-terminal modifications. The BAL strategy was...... assemble the final peptide. One useful application of this strategy is in the synthesis of C-terminal peptide aldehydes. The C-terminal aldehyde is masked as an acetal during synthesis and then conveniently demasked in the final cleavage step to generate the free aldehyde. Another application is in the...

  14. Synthesis of 15 N double labelled urea

    Synthesis of double 15 N labelled urea by reacting 15 N - ammonia with elemental sulfur and carbon monoxide in a pressure vessel is presented. 15 NH3 was produced by H15 NO3 reduction with Dewarda alloy in alkaline solution, or by nitric monoxide reduction with hydrogen on metallic manganese. An average yield of 85% tacking into account 15 N - urea and 15 N ammonium sulfate, produced in the same time, and 99% urea purity (checked by I.R. spectroscopy and mass spectrometry) were obtained. (authors)

  15. Simultaneous acquisition of {sup 13}C{sup {alpha}}-{sup 15}N and {sup 1}H-{sup 15}N-{sup 15}N sequential correlations in proteins: application of dual receivers in 3D HNN

    Chakraborty, Swagata; Paul, Subhradip; Hosur, Ramakrishna V., E-mail: hosur@tifr.res.in [Tata Institute of Fundamental Research, Department of Chemical Sciences (India)

    2012-01-15

    We describe here, adaptation of the HNN pulse sequence for multiple nuclei detection using two independent receivers by utilizing the detectable {sup 13}C{sup {alpha}} transverse magnetization which was otherwise dephased out in the conventional HNN experiment. It enables acquisition of 2D {sup 13}C{sup {alpha}}-{sup 15}N sequential correlations along with the standard 3D {sup 15}N-{sup 15}N-{sup 1}H correlations, which provides directionality to sequential walk in HNN, on one hand, and enhances the speed of backbone assignment, on the other. We foresee that the implementation of dual direct detection opens up new avenues for a wide variety of modifications that would further enhance the value and applications of the experiment, and enable derivation of hitherto impossible information.

  16. Complete resonance assignment for the polypeptide backbone of interleukin 1β using three-dimensional heteronuclear NMR spectroscopy

    The complete sequence-specific assignment of the 15N and 1H backbone resonances of the NMR spectrum of recombinant human interleukin 1β has been obtained by using primarily 15N-1H heteronuclear three-dimensional (3D) NMR techniques in combination with 15N-1H heteronuclear and 1H homonuclear two-dimensional NMR. The fingerprint region of the spectrum was analyzed by using a combination of 3D heteronuclear 1H Hartmann-Hahn 15N-1H multiple quantum coherence (3D HOHAHA-HMQC) and 3D heteronuclear 1H nuclear Overhauser 15N-1H multiple quantum coherence (3D NOESY-HMQC) spectroscopies. The authors show that the problems of amide NH and CαH chemical shift degeneracy that are prevalent for proteins of the size are readily overcome by using the 3D heteronuclear NMR technique. A doubling of some peaks in the spectrum was found to be due to N-terminal heterogeneity of the 15N-labeled protein, corresponding to a mixture of wild-type and des-Ala-1-interleukin 1β. The complete list of 15N and 1H assignments is given for all the amide NH and CαH resonances of all non-proline residues, as well as the 1H assignments for some of the amino acid side chains. This first example of the sequence-specific assignment of a protein using heteronuclear 3D NMR provides a basis for further conformational and dynamic studies of interleukin 1β

  17. Geometry motivated alternative view on local protein backbone structures

    Zacharias, Jan; Knapp, Ernst Walter

    2013-01-01

    We present an alternative to the classical Ramachandran plot (R-plot) to display local protein backbone structure. Instead of the (ϕ, ψ)-backbone angles relating to the chemical architecture of polypeptides generic helical parameters are used. These are the rotation or twist angle ϑ and the helical rise parameter d. Plots with these parameters provide a different view on the nature of local protein backbone structures. It allows to display the local structures in polar (d, ϑ)-coordinates, whi...

  18. The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies

    Šponer, Jiří; Mládek, Arnošt; Šponer, Judit E.; Svozil, Daniel; Zgarbová, M.; Banáš, Pavel; Jurečka, P.; Otyepka, M.

    2012-01-01

    Roč. 14, č. 44 (2012), s. 15257-15277. ISSN 1463-9076 R&D Projects: GA ČR(CZ) GD203/09/H046; GA ČR(CZ) GAP208/10/2302; GA ČR(CZ) GAP208/11/1822; GA ČR(CZ) GAP208/12/1878; GA ČR(CZ) GA203/09/1476; GA ČR(CZ) GBP305/12/G034 Institutional research plan: CEZ:AV0Z50040702 Keywords : DNA * RNA * sugar -phosphate backbone Subject RIV: BO - Biophysics Impact factor: 3.829, year: 2012

  19. Resolution of the 15N balance enigma?

    The enigma of soil nitrogen balance sheets has been discussed for over 40 years. Many reasons have been considered for the incomplete recovery of 15N applied to soils, including sampling uncertainty, gaseous N losses from plants, and entrapment of soil gases. The entrapment of soil gases has been well documented for rice paddy and marshy soils but little or no work appears to have been done to determine entrapment in drained pasture soils. In this study 15N-labelled nitrate was applied to a soil core in a gas-tight glovebox. Water was applied, inducing drainage, which was immediately collected. Dinitrogen and N-2 were determined in the flux through the soil surface, and in the gases released into the glovebox as a result of irrigation or physical destruction of the core. Other components of the N balance were also measured, including soil inorganic-N and organic-N. Quantitative recovery of the applied 15N was achieved when the experiment was terminated 484 h after the 15N-labelled material was applied. Nearly 23% of the 15N was recovered in the glovebox atmosphere as N2 and N2O due to diffusion from the base of the soil core, convective flow after irrigation, and destructive soil sampling. This 15N would normally be unaccounted for using the sampling methodology typically employed in 15N recovery experiments. Copyright (2001) CSIRO Publishing

  20. Biosynthetic uniform 13C,15N-labelling of zervamicin IIB. Complete 13C and 15N NMR assignment.

    Ovchinnikova, Tatyana V; Shenkarev, Zakhar O; Yakimenko, Zoya A; Svishcheva, Natalia V; Tagaev, Andrey A; Skladnev, Dmitry A; Arseniev, Alexander S

    2003-01-01

    Zervamicin IIB is a member of the alpha-aminoisobutyric acid containing peptaibol antibiotics. A new procedure for the biosynthetic preparation of the uniformly 13C- and 15N-enriched peptaibol is described This compound was isolated from the biomass of the fungus-producer Emericellopsis salmosynnemata strain 336 IMI 58330 obtained upon cultivation in the totally 13C, 15N-labelled complete medium. To prepare such a medium the autolysed biomass and the exopolysaccharides of the obligate methylotrophic bacterium Methylobacillus flagellatus KT were used. This microorganism was grown in totally 13C, 15N-labelled minimal medium containing 13C-methanol and 15N-ammonium chloride as the only carbon and nitrogen sources. Preliminary NMR spectroscopic analysis indicated a high extent of isotope incorporation (> 90%) and led to the complete 13C- and 15N-NMR assignment including the stereospecific assignment of Aib residues methyl groups. The observed pattern of the structurally important secondary chemical shifts of 1H(alpha), 13C=O and 13C(alpha) agrees well with the previously determined structure of zervamicin IIB in methanol solution. PMID:14658801

  1. HN-NCA heteronuclear TOCSY-NH experiment for {sup 1}H{sup N} and {sup 15}N sequential correlations in ({sup 13}C, {sup 15}N) labelled intrinsically disordered proteins

    Wiedemann, Christoph; Goradia, Nishit; Häfner, Sabine [Leibniz Institute for Age Research, Fritz Lipmann Institute, Research Group Biomolecular NMR Spectroscopy (Germany); Herbst, Christian [Ubon Ratchathani University, Department of Physics, Faculty of Science (Thailand); Görlach, Matthias; Ohlenschläger, Oliver; Ramachandran, Ramadurai, E-mail: raman@fli-leibniz.de [Leibniz Institute for Age Research, Fritz Lipmann Institute, Research Group Biomolecular NMR Spectroscopy (Germany)

    2015-10-15

    A simple triple resonance NMR experiment that leads to the correlation of the backbone amide resonances of each amino acid residue ‘i’ with that of residues ‘i−1’ and ‘i+1’ in ({sup 13}C, {sup 15}N) labelled intrinsically disordered proteins (IDPs) is presented. The experimental scheme, {HN-NCA heteronuclear TOCSY-NH}, exploits the favourable relaxation properties of IDPs and the presence of {sup 1}J{sub CαN} and {sup 2}J{sub CαN} couplings to transfer the {sup 15}N{sub x} magnetisation from amino acid residue ‘i’ to adjacent residues via the application of a band-selective {sup 15}N–{sup 13}C{sup α} heteronuclear cross-polarisation sequence of ∼100 ms duration. Employing non-uniform sampling in the indirect dimensions, the efficacy of the approach has been demonstrated by the acquisition of 3D HNN chemical shift correlation spectra of α-synuclein. The experimental performance of the RF pulse sequence has been compared with that of the conventional INEPT-based HN(CA)NH pulse scheme. As the availability of data from both the HCCNH and HNN experiments will make it possible to use the information extracted from one experiment to simplify the analysis of the data of the other and lead to a robust approach for unambiguous backbone and side-chain resonance assignments, a time-saving strategy for the simultaneous collection of HCCNH and HNN data is also described.

  2. Synthesis and NMR characterization of (15N)taurine [2-(15N)aminoethanesulfonic acid

    The title compound was prepared in three steps with 55% overall yield starting from potassium (15N)phthalimide. The synthetic route involved reaction with 1,2-dibromoethane, hydrolysis of the resulting N-(2-bromoethyl) (15N)phthalimide with HBr and treatment of the 2-bromoethyl(15N)amine thus formed with sodium sulphite. The product was characterized by 13C, 1H and 15N NMR spectroscopy. The absolute coupling constants of 15N with the 13C nuclei and the non-exchanging protons were determined and an unambiguous assignment of the proton signals obtained. (author)

  3. Hyperpolarized 15N-pyridine Derivatives as pH-Sensitive MRI Agents

    Weina Jiang; Lloyd Lumata; Wei Chen; Shanrong Zhang; Zoltan Kovacs; A. Dean Sherry; Chalermchai Khemtong

    2015-01-01

    Highly sensitive MR imaging agents that can accurately and rapidly monitor changes in pH would have diagnostic and prognostic value for many diseases. Here, we report an investigation of hyperpolarized 15N-pyridine derivatives as ultrasensitive pH-sensitive imaging probes. These molecules are easily polarized to high levels using standard dynamic nuclear polarization (DNP) techniques and their 15N chemical shifts were found to be highly sensitive to pH. These probes displayed sharp 15N resona...

  4. Reduced dimensionality tailored HN(C)N experiments for facile backbone resonance assignment of proteins through unambiguous identification of sequential HSQC peaks

    Kumar, Dinesh

    2013-12-01

    Two novel reduced dimensionality (RD) tailored HN(C)N [S.C. Panchal, N.S. Bhavesh, R.V. Hosur, Improved 3D triple resonance experiments, HNN and HN(C)N, for HN and 15N sequential correlations in (13C, 15N) labeled proteins: application to unfolded proteins, J. Biomol. NMR 20 (2001) 135-147] experiments are proposed to facilitate the backbone resonance assignment of proteins both in terms of its accuracy and speed. These experiments - referred here as (4,3)D-hNCOcaNH and (4,3)D-hNcoCANH - exploit the linear combination of backbone 15N and 13C‧/13Cα chemical shifts simultaneously to achieve higher peak dispersion and randomness along their respective F1 dimensions. Simply, this has been achieved by modulating the backbone 15N(i) chemical shifts with that of 13C‧ (i - 1)/13Cα (i - 1) spins following the established reduced dimensionality NMR approach [T. Szyperski, D.C. Yeh, D.K. Sukumaran, H.N. Moseley, G.T. Montelione, Reduced-dimensionality NMR spectroscopy for high-throughput protein resonance assignment, Proc. Natl. Acad. Sci. USA 99 (2002) 8009-8014]. Though the modification is simple it has resulted an ingenious improvement of HN(C)N both in terms of peak dispersion and easiness of establishing the sequential connectivities. The increased dispersion along F1 dimension solves two purposes here: (i) resolves the ambiguities arising because of degenerate 15N chemical shifts and (ii) reduces the signal overlap in F2(15N)-F3(1H) planes (an important requisite in HN(C)N based assignment protocol for facile and unambiguous identification of sequentially connected HSQC peaks). The performance of both these experiments and the assignment protocol has been demonstrated using bovine apo Calbindin-d9k (75 aa) and urea denatured UNC60B (a 152 amino acid ADF/cofilin family protein of Caenorhabditis elegans), as representatives of folded and unfolded protein systems, respectively.

  5. The effect of organic matter and nitrification inhibitor on 15 N H4 and 15 N O3 absorption by the maize

    The effect of the forms 15 N H4 and 15 N O3 in presence or absence of organic matter and of the nitrification inhibitor AM (2-amino-4-chloro-6-methyl-pyrimidine) in dry matter weight and nitrogen content of the plant derived from soil and form fertilizer is studied. The experiment was carried out in greenhouse and the test plant was the hybrid Maize Centralmex . The fertilizers (15 N H4)2 S O4 and Na15 N O3, were added in two levels: 40 and 120 Kg N/ha, with 1,02% of N and 1,4% of 15 N in excess, respectively. Three soils of different physical and chemical characteristics were used; Regosol intergrade, Latosol Roxo and Podzolized de Lins e Marilia var. Marilia. (M.A.C.)

  6. Measurement of 15N relaxation rates in perdeuterated proteins by TROSY-based methods

    While extracting dynamics parameters from backbone 15N relaxation measurements in proteins has become routine over the past two decades, it is increasingly recognized that accurate quantitative analysis can remain limited by the potential presence of systematic errors associated with the measurement of 15N R1 and R2 or R1ρ relaxation rates as well as heteronuclear 15N-{1H} NOE values. We show that systematic errors in such measurements can be far larger than the statistical error derived from either the observed signal-to-noise ratio, or from the reproducibility of the measurement. Unless special precautions are taken, the problem of systematic errors is shown to be particularly acute in perdeuterated systems, and even more so when TROSY instead of HSQC elements are used to read out the 15N magnetization through the NMR-sensitive 1H nucleus. A discussion of the most common sources of systematic errors is presented, as well as TROSY-based pulse schemes that appear free of systematic errors to the level of 2′/R1′ ratios fit an axially symmetric diffusion tensor with a Pearson’s correlation coefficient of 0.97, comparable to fits obtained for backbone amide RDCs to the Saupe matrix.

  7. Fields of application and results of analytic procedures with 15N in pediatric alimentary research

    Investigation of protein metabolism in nutritional pediatric research by means of 15N tracer techniques has been relatively seldom used up to now. 15N labelled compounds for these purposes are not injurious to health. The technique is based on oral or intravenous application of the tracer substances and on 15N analysis of the urine fractions. The subsequent calculation of protein synthesis and breakdown rate, turnover and reutilisation of amino acids from protein breakdown as well as the size of the metabolic pool offers detailed information of protein metabolism. Determination of these parameters was performed in infants on mother's milk and formula feeding and on chemically defined diet. As an example of utilisation of D-amino acids for protein synthesis the 15N-D-phenylalanin retention on parenteral nutrition was found to be 33% of the applied dosis at an average. An oral 15N glycine loading test proved to be of value for the prediction of the therapeutic effect of human growth hormon in numerous types of dwarfism. Further application of 15N tracer technique dealt with utilisation of 15N urea for bacterial protein synthesis of the intestinal flora and with incorporation of 15N from 15N glycine and 15N lysine into the jejunal mucosa for measuring the enterocyte regeneration. (author)

  8. CPMG sequences with enhanced sensitivity to chemical exchange

    Improved relaxation-compensated Carr-Purcell-Meiboom-Gill pulse sequences are reported for studying chemical exchange of backbone 15N nuclei. In contrast to the original methods [J. P. Loria, M. Rance, and A. G. Palmer, J. Am. Chem. Soc.121, 2331-2332 (1999)], phenomenological relaxation rate constants obtained using the new sequences do not contain contributions from 1H-1H dipole-dipole interactions. Consequently, detection and quantification of chemical exchange processes are facilitated because the relaxation rate constant in the limit of fast pulsing can be obtained independently from conventional 15N spin relaxation measurements. The advantages of the experiments are demonstrated using basic pancreatic trypsin inhibitor

  9. 15N in biological nitrogen fixation studies

    A bibliography with 298 references on the use of the stable nitrogen isotope 15N in the research on the biological fixation of dinitrogen is presented. The literature pertaining to this bibliography covers the period from 1975 to the middle of 1985. (author)

  10. Efficient identification of amino acid types for fast protein backbone assignments

    We describe a procedure that allows for very efficient identification of amino acid types in proteins by selective 15N-labeling. The usefulness of selective incorporation of 15N-labeled amino acids into proteins for the backbone assignment has been recognized for several years. However, widespread use of this method has been hindered by the need to purify each selectively labeled sample and by the relatively high cost of labeling with 15N-labeled amino acids. Here we demonstrate that purification of the selectively 15N-labeled samples is not necessary and that background-free HSQC spectra containing only the peaks of the overexpressed heterologous protein can be obtained in crude lysates from as little as 100 ml cultures, thus saving time and money. This method can be used for fast and automated backbone assignment of proteins

  11. Getting started with Backbone Marionette

    Armendariz, Raymundo

    2014-01-01

    This book is written with an easy-to-understand approach with the intention of giving small but concrete examples that will help you to quickly understand each component of Marionette. Follow along as we work together to build a practical application using Backbone Marionette.If you are a web application developer interested in using Backbone Marionette for a real-life project, then this book is for you. As a prerequisite, knowledge of JavaScript and a working knowledge of Backbone.js is required.

  12. 15N2 incorporation by rhizosphere soil

    Heterotrophic nitrogen fixation by rhizosphere soil samples from 20 rice cultivars grown under uniform field conditions was estimated employing 15N-tracer technique. Rhizosphere soil samples from different rice cultivars showed striking differences with regard to their ability to incorporate 15N2. Rhizosphere samples from rice straw-amended (3 and 6 tons/ha) soil exhibited more pronounced nitrogen-fixing activity than the samples form unamended soil; while the activity of the rhizosphere samples from soil receiving combined nitrogen (40 and 80 kg N/ha) was relatively low. However, the inhibitory effect of combined nitrogen was not expressed in the presence of rice straw at 6 tons/ha. Results suggest that plant variety, application of combined nitrogen and organic matter influence the rhizosphere nitrogen fixation. (orig.)

  13. Orientational constraints as three-dimensional structural constraints from chemical shift anisotropy: the polypeptide backbone of gramicidin A in a lipid bilayer.

    Mai, W.; Hu, W; Wang, C; Cross, T A

    1993-01-01

    Chemical shifts observed from samples that are uniformly aligned with respect to the magnetic field can be used as very high-resolution structural constraints. This constraint takes the form of an orientational constraint rather than the more familiar distance constraint. The accuracy of these constraints is dependent upon the quality of the tensor characterization. Both tensor element magnitudes and tensor orientations with respect to the molecular frame need to be considered. Here these con...

  14. 15N-labed glycine synthesis

    Claudinéia R. O. Tavares; José A. Bendassolli; Fernando Coelho; Carlos R. Sant Ana Filho; Clelber V. Prestes

    2006-01-01

    This work describes a method for 15N-isotope-labeled glycine synthesis, as well as details about a recovery line for nitrogen residues. To that effect, amination of alpha-haloacids was performed, using carboxylic chloroacetic acid and labeled aqueous ammonia (15NH3). Special care was taken to avoid possible 15NH3 losses, since its production cost is high. In that respect, although the purchase cost of the 13N-labeled compound (radioactive) is lower, the stable tracer produced constitutes an i...

  15. Sources and transformations of N in reclaimed coastal tidelands: evidence from soil δ15N data

    Kwak, Jin-Hyeob; Choi, Woo-Jung; Lim, Sang-Sun; Lee, Seung-Heon; Lee, Sang-Mo; Chang, Scott X.; Jung, Jae-Woon; Yoon, Kwang-Sik; Choi, Soo-Myung

    2008-01-01

    Electrical conductivity of saturated soil extracts (ECe) in three reclaimed tideland (RTL) soils on the west coast of Korea decreased with time since reclamation, indicating natural desalinization through leaching of salts by precipitation water. Soil N concentration increased with decreasing ECe. With the increase in soil N concentration, the δ15N decreased, likely caused by the input of 15N-depleted N sources. As N2-fixing plant species were found in the oldest RTL, atmospheric N2 fixation likely contributed to the increase in soil N concentration in the oldest RTL. Negative δ15N (-7.1 to -2.0‰) of total inorganic N (NH4 ++NO3 -) and published data on N deposition near the study area indicate that atmospheric N deposition might be another source of N in the RTLs. Meanwhile, the consistently negative δ15N of soil NO3 - excluded N input from chemical fertilizer through groundwater flow as a potential N source, since NO3 - in groundwater generally have a positive δ15N. The patterns of δ15N of NH4 + (+2.3 to +5.1‰) and NO3 - (-9.2 to -5.0‰) suggested that nitrification was an active process that caused 15N enrichment in NH4 + but denitrification was probably minimal which would otherwise have caused 15N enrichment in NO3 -. A quantitative approach on N budget would provide a better understanding of soil N dynamics in the studied RTLs.

  16. Fuzzy logic control of 15 N separation plant

    The process of 15 N separation by chemical exchange in Nitrox system is automatically maintained in the optimal operation conditions using a computerized control. The automatic control leads to a maximum production of 15 N with a minimum of raw materials and energy consumption.. The control objective was achieved by considering two forms of knowledge: 1. objective knowledge, which uses the control engineering based on mathematical model of the separation process; 2. subjective knowledge, which represents linguistic information, very difficult to quantify using classical mathematics - e.g., the rule of HNO3 solution and SO2 flow rates adjustment in order to maintain a proper height and position of chemical reaction zone in the product refluxer. The above mentioned two types of knowledge were coordinated in a logical way using fuzzy logic control system which has the possibility to handle simultaneously numerical data and linguistic knowledge. In order to map input data vector into a scalar output, i.e., numbers to numbers a front-end 'fuzzifier' and a rear-end 'defuzzifier' was added to the usual fuzzy logic model. The inference engine of the control system maps the input fuzzy set into the output one. The inferential procedure maintains the isotope separation process in the optimal operation conditions. (author)

  17. Effect of protein restriction on (15)N transfer from dietary [(15)N]alanine and [(15)N]Spirulina platensis into urea.

    Hamadeh, M J; Hoffer, L J

    2001-08-01

    Six normal men consumed a mixed test meal while adapted to high (1.5 g. kg(-1) x day(-1)) and low (0.3 g. kg(-1) x day(-1)) protein intakes. They completed this protocol twice: when the test meals included 3 mg/kg of [(15)N]alanine ([(15)N]Ala) and when they included 30 mg/kg of intrinsically labeled [(15)N]Spirulina platensis ([(15)N]SPI). Six subjects with insulin-dependent diabetes mellitus (IDDM) receiving conventional insulin therapy consumed the test meal with added [(15)N]Ala while adapted to their customary high-protein diet. Protein restriction increased serum alanine, glycine, glutamine, and methionine concentrations and reduced those of leucine. Whether the previous diet was high or low in protein, there was a similar increase in serum alanine, methionine, and branched-chain amino acid concentrations after the test meal and a similar pattern of (15)N enrichment in serum amino acids for a given tracer. When [(15)N]Ala was included in the test meal, (15)N appeared rapidly in serum alanine and glutamine, to a minor degree in leucine and isoleucine, and not at all in other circulating amino acids. With [(15)N]SPI, there was a slow appearance of the label in all serum amino acids analyzed. Despite the different serum amino acid labeling, protein restriction reduced the postmeal transfer of dietary (15)N in [(15)N]Ala or [(15)N]SPI into [(15)N]urea by similar amounts (38 and 43%, respectively, not significant). The response of the subjects with IDDM was similar to that of the normal subjects. Information about adaptive reductions in dietary amino acid catabolism obtained by adding [(15)N]Ala to a test meal appears to be equivalent to that obtained using an intrinsically labeled protein tracer. PMID:11440912

  18. Nitrogen cycling in an extreme hyperarid environment inferred from δ15N analyses of plants, soils and herbivore diet

    Díaz, Francisca P.; Matías Frugone; Gutiérrez, Rodrigo A.; Claudio Latorre

    2016-01-01

    Climate controls on the nitrogen cycle are suggested by the negative correlation between precipitation and δ15N values across different ecosystems. For arid ecosystems this is unclear, as water limitation among other factors can confound this relationship. We measured herbivore feces, foliar and soil δ15N and δ13C values and chemically characterized soils (pH and elemental composition) along an elevational/climatic gradient in the Atacama Desert, northern Chile. Although very positive δ15N va...

  19. Change of 15N natural abundance (δ15N) in a forest soil receiving elevated N deposition

    Natural abundance of 15N15N) has been used to interpret N mineralization in forest ecosystems. Forest litter typically has depleted δ15N values ranging from -8 to 0 per mille and δ15N values of organic N in forest soil profiles become more enriched with depth. This study investigated (1) the change of δ15N and total N with depth, and (2) the relation between the change of δ15N within the 0 to 10, 10 to 20 and 20 to 30 cm intervals of the mineral layer and the N mineralization rates in these layers

  20. The 15N-enrichment in dark clouds and Solar System objects

    Hily-Blant, Pierre; Faure, Alexandre; Quirico, Eric

    2013-01-01

    The line intensities of the fundamental rotational transitions of H13CN and HC15N were observed towards two prestellar cores, L183 and L1544, and lead to molecular isotopic ratios 140 6 14N/15N 6 250 and 140 6 14N/15N 6 360, respectively. The range of values reflect genuine spatial variations within the cores. A comprehensive analysis of the available measurements of the nitrogen isotopic ratio in prestellar cores show that molecules carrying the nitrile functional group appear to be systematically 15N-enriched com- pared to those carrying the amine functional group. A chemical origin for the differential 15N-enhance- ment between nitrile- and amine-bearing interstellar molecules is proposed. This sheds new light on several observations of Solar System objects: (i) the similar N isotopic fractionation in Jupiter's NH3 and solar wind N+; (ii) the 15N-enrichments in cometary HCN and CN (that might represent a direct inter- stellar inheritance); and (iii) 15N-enrichments observed in organics in primitive cosmoma...

  1. Application of unsymmetrical indirect covariance NMR methods to the computation of the (13)C (15)N HSQC-IMPEACH and (13)C (15)N HMBC-IMPEACH correlation spectra.

    Martin, Gary E; Hilton, Bruce D; Irish, Patrick A; Blinov, Kirill A; Williams, Antony J

    2007-10-01

    Utilization of long-range (1)H--(15)N heteronuclear chemical shift correlation has continually grown in importance since the first applications were reported in 1995. More recently, indirect covariance NMR methods have been introduced followed by the development of unsymmetrical indirect covariance processing methods. The latter technique has been shown to allow the calculation of hyphenated 2D NMR data matrices from more readily acquired nonhyphenated 2D NMR spectra. We recently reported the use of unsymmetrical indirect covariance processing to combine (1)H--(13)C GHSQC and (1)H--(15)N GHMBC long-range spectra to yield a (13)C--(15)N HSQC-HMBC chemical shift correlation spectrum that could not be acquired in a reasonable period of time without resorting to (15)N-labeled molecules. We now report the unsymmetrical indirect covariance processing of (1)H--(13)C GHMBC and (1)H--(15)N IMPEACH spectra to afford a (13)C--(15)N HMBC-IMPEACH spectrum that has the potential to span as many as six to eight bonds. Correlations for carbon resonances long-range coupled to a protonated carbon in the (1)H--(13)C HMBC spectrum are transferred via the long-range (1)H--(15)N coupling pathway in the (1)H--(15)N IMPEACH spectrum to afford a much broader range of correlation possibilities in the (13)C--(15)N HMBC-IMPEACH correlation spectrum. The indole alkaloid vincamine is used as a model compound to illustrate the application of the method. PMID:17729230

  2. Binding of oxytocin and 8-arginine-vasopressin to neurophysin studied by /sup 15/N NMR using magnetization transfer and indirect detection via protons

    Live, D.H.; Cowburn, D.

    1987-10-06

    NMR was used to monitor the binding to neurophysin of oxytocin and 8-arginine-vasopressin, /sup 15/N labeling being used to identify specific backbone /sup 15/N and /sup 1/H signals. The most significant effects of binding were large downfield shifts in the amino nitrogen resonance of Phe-3 of vasopressin and in its associated proton, providing evidence that the peptide bond between residues 2 and 3 of the hormones is hydrogen-bonded to the protein within hormone-neurophysin complexes. Suggestive evidence for hydrogen bonding of the amino nitrogen of Tyr-2 was also obtained in the form of decreased proton exchange rates on binding; however, the chemical shift changes of this nitrogen and its associated proton indicated that such hydrogen bonding, if present, is probably weak. Shifts in the amino nitrogen of Asn-5 and in the -NH protons of both Asn-5 and Cys-6 demonstrated that these residues are significantly perturbed by binding, suggesting conformational changes of the ring on binding and/or the presence of binding sites on the hormone outside the 1-3 region. No support was obtained for the thesis that there is a significant second binding site for vasopressin on each neutrophysin chain. The behavior of both oxytocin and vasopressin on binding was consistent with formation of 1:1 complexes in slow exchange with the free state under most pH conditions. At low pH there was evidence of an increased exchange rate. Additionally, broadening of /sup 15/N resonances in the bound state at low pH occurred without a corresponding change in the resonances of equilibrating free hormone. The results suggest significant conformational alteration in neurophysin-hormone complexes at low pH possibly associated with protonation of the carboxyl group of the hormone-protein salt bridge.

  3. Nitrogen cycling in an extreme hyperarid environment inferred from δ15N analyses of plants, soils and herbivore diet

    Díaz, Francisca P.; Frugone, Matías; Gutiérrez, Rodrigo A.; Latorre, Claudio

    2016-03-01

    Climate controls on the nitrogen cycle are suggested by the negative correlation between precipitation and δ15N values across different ecosystems. For arid ecosystems this is unclear, as water limitation among other factors can confound this relationship. We measured herbivore feces, foliar and soil δ15N and δ13C values and chemically characterized soils (pH and elemental composition) along an elevational/climatic gradient in the Atacama Desert, northern Chile. Although very positive δ15N values span the entire gradient, soil δ15N values show a positive correlation with aridity as expected. In contrast, foliar δ15N values and herbivore feces show a hump-shaped relationship with elevation, suggesting that plants are using a different N source, possibly of biotic origin. Thus at the extreme limits of plant life, biotic interactions may be just as important as abiotic processes, such as climate in explaining ecosystem δ15N values.

  4. Nitrogen cycling in an extreme hyperarid environment inferred from δ(15)N analyses of plants, soils and herbivore diet.

    Díaz, Francisca P; Frugone, Matías; Gutiérrez, Rodrigo A; Latorre, Claudio

    2016-01-01

    Climate controls on the nitrogen cycle are suggested by the negative correlation between precipitation and δ(15)N values across different ecosystems. For arid ecosystems this is unclear, as water limitation among other factors can confound this relationship. We measured herbivore feces, foliar and soil δ(15)N and δ(13)C values and chemically characterized soils (pH and elemental composition) along an elevational/climatic gradient in the Atacama Desert, northern Chile. Although very positive δ(15)N values span the entire gradient, soil δ(15)N values show a positive correlation with aridity as expected. In contrast, foliar δ(15)N values and herbivore feces show a hump-shaped relationship with elevation, suggesting that plants are using a different N source, possibly of biotic origin. Thus at the extreme limits of plant life, biotic interactions may be just as important as abiotic processes, such as climate in explaining ecosystem δ(15)N values. PMID:26956399

  5. 15N NMR spectroscopy of Pseudomonas cytochrome c-551

    15N-1H correlation spectroscopy with detection at the 1H frequency has been used at natural abundance to detect nitrogen nuclei bonded to protons in the ferrocytochrome c-551 from Pseudomonas aeruginosa (ATCC 19429). Side-chain aromatic nitrogen, main-chain amides, and side-chain amides have been assigned to specific residues by comparison to previous proton assignments. Assignment ambiguities arising from overlap in the proton dimension have been resolved by examining spectra as a function of temperature and pH. Nitrogen chemical shifts are reported at pH 4.6 and 9.4 and three temperatures, 32, 50, and 60 degree C. Significant differences arise from the observed protein shifts and expected shifts in the random coil polypeptide

  6. Simultaneous acquisition of 13Cα–15N and 1H–15N–15N sequential correlations in proteins: application of dual receivers in 3D HNN

    We describe here, adaptation of the HNN pulse sequence for multiple nuclei detection using two independent receivers by utilizing the detectable 13Cα transverse magnetization which was otherwise dephased out in the conventional HNN experiment. It enables acquisition of 2D 13Cα–15N sequential correlations along with the standard 3D 15N–15N–1H correlations, which provides directionality to sequential walk in HNN, on one hand, and enhances the speed of backbone assignment, on the other. We foresee that the implementation of dual direct detection opens up new avenues for a wide variety of modifications that would further enhance the value and applications of the experiment, and enable derivation of hitherto impossible information.

  7. 15N fractionation in star-forming regions and Solar System objects

    Wirström, Eva; Milam, Stefanie; Adande, Gilles; Charnley, Steven B.; Cordiner, Martin A.

    2015-08-01

    A central issue for understanding the formation and evolution of matter in the early Solar System is the relationship between the chemical composition of star-forming interstellar clouds and that of primitive Solar System materials. The pristine molecular content of comets, interplanetary dust particles and carbonaceous chondrites show significant bulk nitrogen isotopic fractionation relative to the solar value, 14N/15N ~ 440. In addition, high spatial resolution measurements in primitive materials locally show even more extreme enhancements of 14N/15N natal molecular cloud core and the outer protosolar nebula. Indeed, early chemical models of gas-phase ion-molecule nitrogen fractionation showed that HCN and HNC (nitriles) can hold significant 15N enrichments in cold dark clouds where CO is depleted onto dust grains. In addition, 15N fractionation in nitriles and amines (NH2, NH3) follow different chemical pathways. More recently we have shown that once the spin-state dependence in rates of reactions with H2 is included in the models, amines can either be enhanced or depleted in 15N, depending on the core’s evolutionary stage. Observed 15N fractionation in amines and nitriles therefore cannot be expected to be the same, instead their ratio is a potential chemical clock.Observations of molecular isotope ratios in dark cores are challenging. Limited published results in general show higher 15N/14N ratios in HCN and HNC than ammonia, but more measurements are necessary to confirm these trends. We will present recent results from our ongoing observing campaign of 14N/15N isotopic ratios in HCN, HNC and NH3 in dense cores and protostars which seem consistent with significant fractionation in nitriles as compared to other molecules in each object. The few 14N/15N ratios observed in N2H+ are similar to those in NH3, contrary to our model results which predict a significant 15N enhancement in N2 and N2H+. Model upgrades which may address this discrepancy will be

  8. Study of protein metabolism and cell proliferation using 15N

    Investigations of nitrogen and protein metabolism with the stable isotope 15N were carried out in 11 patients with arteriosclerosis and 7 healthy controls. After oral application of 3 g 15NH4Cl (95 At% 15N) per 70 kg body weight the incorporation of the isotope 15N in plasma proteins and blood cells and the 15N elimination in urine were followed up. Retardations of 15N elimination, an accelerated incorporation of 15N in fibrin and a retarded 15N incorporation in platelet protein were observed in patients with arteriosclerosis. The described method enables complex assertions about protein metabolism of the whole body and so represents a possibility to evaluate objectively the influence of an intervention on metabolism. (author)

  9. Backbone dynamics of the human CC-chemokine eotaxin

    Eotaxin is a CC chemokine with potent chemoattractant activity towards eosinophils. 15N NMR relaxation data have been used to characterize the backbone dynamics of recombinant human eotaxin. 15N longitudinal (R1) and transverse (R2) auto relaxation rates, heteronuclear 1H-15N steady-state NOEs, and transverse cross-relaxation rates (ηxy) were obtained at 30 deg. C for all resolved backbone secondary amide groups using 1 H-detected two-dimensional NMR experiments. Ratios of transverse auto and cross relaxation rates were used to identify NH groups influenced by slow conformational rearrangement. Relaxation data were fit to the extended model free dynamics formalism, yielding parameters describing axially symmetric molecular rotational diffusion and the internal dynamics of each NH group. The molecular rotational correlation time (τm) is 5.09±0.02 ns, indicating that eotaxin exists predominantly as a monomer under the conditions of the NMR study. The ratio of diffusion rates about unique and perpendicular axes (Dparallel/Dperpendicular) is 0.81±0.02. Residues with large amplitudes of subnanosecond motion are clustered in the N-terminal region (residues 1-19), the C-terminus (residues 68-73) and the loop connecting the first two β-strands (residues 30-37). N-terminal flexibility appears to be conserved throughout the chemokine family and may have implications for the mechanism of chemokine receptor activation. Residues exhibiting significant dynamics on the microsecond-millisecond time scale are located close to the two conserved disulfide bonds, suggesting that these motions may be coupled to disulfide bond isomerization

  10. 15N-{1H} NOE experiment at high magnetic field strengths

    The heteronuclear 15N-{1H} NOE values are typically determined by taking the ratio of 15N signal intensities recorded in the presence and absence of 1H saturation prior to evolution of 15N magnetization. Since the intensity ratio of two independent experiments is taken, complete recovery of 15N magnetization during the scan repetition delay is critical to obtain reliable NOE values. Because it may not be practical to wait for the complete recovery of magnetization at high magnetic fields, Solomon equations may be used to correct measured NOE values. Here, based on experiments and simulations, we show that since the cross-correlation between 1H-15N dipole and 15N chemical shift anisotropy becomes significant at high fields for small or deuterated proteins, measured NOE values can not be accurately corrected based on the Solomon equations. We also discuss ranges of rotational correlation times and proton spin-flip rate, in which the NOE values can be corrected by the equations

  11. 1H, 13C, and 15N backbone and side chain resonance assignments of thermophilic Geobacillus kaustophilus cyclophilin-A

    Holliday, Michael; Zhang, Fengli; Isern, Nancy G.; Armstrong, Geoffrey S.; Eisenmesser, Elan Z.

    2014-04-01

    Cyclophilins catalyze the reversible peptidyl-prolyl isomerization of their substrates and are present across all kingdoms of life from humans to bacteria. Although numerous biological roles have now been discovered for cyclophilins, their function was initially ascribed to their chaperone-like activity in protein folding where they catalyze the often rate-limiting step of proline isomerization. This chaperone-like activity may be especially important under extreme conditions where cyclophilins are often over expressed, such as in tumors for human cyclophilins {Lee, 2010 #1167}, but also in organisms that thrive under extreme conditions, such as theromophilic bacteria. Moreover, the reversible nature of the peptidyl-prolyl isomerization reaction catalyzed by cyclophilins has allowed these enzymes to serve as model systems for probing the role of conformational changes during catalytic turnover {Eisenmesser, 2002 #20;Eisenmesser, 2005 #203}. Thus, we present here the resonance assignments of a thermophilic cyclophilin from Geobacillus kaustophilus derived from deep-sea sediment {Takami, 2004 #1384}. This thermophilic cyclophilin may now be studied at a variety of temperatures to provide insight into the comparative structure, dynamics, and catalytic mechanism of cyclophilins.

  12. Mechanism of the bisphosphatase reaction of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase probed by (1)H-(15)N NMR spectroscopy.

    Okar, D A; Live, D H; Devany, M H; Lange, A J

    2000-08-15

    The histidines in the bisphosphatase domain of rat liver 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase were labeled with (15)N, both specifically at N1' and globally, for use in heteronuclear single quantum correlation (HSQC) NMR spectroscopic analyses. The histidine-associated (15)N resonances were assigned by correlation to the C2' protons which had been assigned previously [Okar et al., Biochemistry 38, 1999, 4471-79]. Acquisition of the (1)H-(15)N HSQC from a phosphate-free sample demonstrated that the existence of His-258 in the rare N1' tautomeric state is dependent upon occupation of the phosphate binding site filled by the O2 phosphate of the substrate, fructose-2,6-bisphosphate, and subsequently, the phosphohistidine intermediate. The phosphohistidine intermediate is characterized by two hydrogen bonds involving the catalytic histidines, His-258 and His-392, which are directly observed at the N1' positions of the imidazole rings. The N1' of phospho-His-258 is protonated ((1)H chemical shift, 14.0 ppm) and hydrogen bonded to the backbone carbonyl of Gly-259. The N1' of cationic His-392 is hydrogen bonded ((1)H chemical shift, 13.5 ppm) to the phosphoryl moiety of the phosphohistidine. The existence of a protonated phospho-His-258 intermediate and the observation of a fairly strong hydrogen bond to the same phosphohistidine implies that hydrolysis of the covalent intermediate proceeds without any requirement for an "activated" water. Using the labeled histidines as probes of the catalytic site mutation of Glu-327 to alanine revealed that, in addition to its function as the proton donor to fructose-6-phosphate during formation of the transient phosphohistidine intermediate at the N3' of His-258, this residue has a significant role in maintaining the structural integrity of the catalytic site. The (1)H-(15)N HSQC data also provide clear evidence that despite being a surface residue, His-446 has a very acidic pK(a), much less than 6.0. On the basis of

  13. MERA: a webserver for evaluating backbone torsion angle distributions in dynamic and disordered proteins from NMR data

    Mantsyzov, Alexey B. [M.V. Lomonosov Moscow State University, Faculty of Fundamental Medicine (Russian Federation); Shen, Yang; Lee, Jung Ho [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Hummer, Gerhard [Max Planck Institute of Biophysics (Germany); Bax, Ad, E-mail: bax@nih.gov [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

    2015-09-15

    MERA (Maximum Entropy Ramachandran map Analysis from NMR data) is a new webserver that generates residue-by-residue Ramachandran map distributions for disordered proteins or disordered regions in proteins on the basis of experimental NMR parameters. As input data, the program currently utilizes up to 12 different parameters. These include three different types of short-range NOEs, three types of backbone chemical shifts ({sup 15}N, {sup 13}C{sup α}, and {sup 13}C′), six types of J couplings ({sup 3}J{sub HNHα}, {sup 3}J{sub C′C′}, {sup 3}J{sub C′Hα}, {sup 1}J{sub HαCα}, {sup 2}J{sub CαN} and {sup 1}J{sub CαN}), as well as the {sup 15}N-relaxation derived J(0) spectral density. The Ramachandran map distributions are reported in terms of populations of their 15° × 15° voxels, and an adjustable maximum entropy weight factor is available to ensure that the obtained distributions will not deviate more from a newly derived coil library distribution than required to account for the experimental data. MERA output includes the agreement between each input parameter and its distribution-derived value. As an application, we demonstrate performance of the program for several residues in the intrinsically disordered protein α-synuclein, as well as for several static and dynamic residues in the folded protein GB3.

  14. MERA: a webserver for evaluating backbone torsion angle distributions in dynamic and disordered proteins from NMR data

    MERA (Maximum Entropy Ramachandran map Analysis from NMR data) is a new webserver that generates residue-by-residue Ramachandran map distributions for disordered proteins or disordered regions in proteins on the basis of experimental NMR parameters. As input data, the program currently utilizes up to 12 different parameters. These include three different types of short-range NOEs, three types of backbone chemical shifts (15N, 13Cα, and 13C′), six types of J couplings (3JHNHα, 3JC′C′, 3JC′Hα, 1JHαCα, 2JCαN and 1JCαN), as well as the 15N-relaxation derived J(0) spectral density. The Ramachandran map distributions are reported in terms of populations of their 15° × 15° voxels, and an adjustable maximum entropy weight factor is available to ensure that the obtained distributions will not deviate more from a newly derived coil library distribution than required to account for the experimental data. MERA output includes the agreement between each input parameter and its distribution-derived value. As an application, we demonstrate performance of the program for several residues in the intrinsically disordered protein α-synuclein, as well as for several static and dynamic residues in the folded protein GB3

  15. Synthesis and NMR of {sup 15}N-labeled DNA fragments

    Jones, R.A. [Rutgers, The State Univ. of New Jersey, Piscataway, NJ (United States)

    1994-12-01

    DNA fragments labeled with {sup 15}N at the ring nitrogens and at the exocyclic amino groups can be used to obtain novel insight into interactions such as base pairing, hydration, drug binding, and protein binding. A number of synthetic routes to {sup 15}N-labeled pyrimidine nucleosides, purines, and purine nucleosides have been reported. Moreover, many of these labeled bases or monomers have been incorporated into nucleic acids, either by chemical synthesis or by biosynthetic procedures. The focus of this chapter will be on the preparation of {sup 15}N-labeled purine 2{prime}-deoxynucleosides, their incorporation into DNA fragments by chemical synthesis, and the results of NMR studies using these labeled DNA fragments.

  16. Synthesis of [α-15N]-dl-tryptophan

    [α-15N]-dl-tryptophan was synthesized by the use of Al-Ni alloy catalytic hydrogenation from 15N-glycine via several steps. The overall yield of the final product was 46.9% and the abundance of 15N was about 93%. The physicochemical properties of the synthetic compound obtained were the same as those of the standard tryptophan. Its structure were confirmed by the elemental analyses, MS, UV and paper chromatography

  17. 15N tracer methodology for absorption studies in nutrition research

    Proceeding from 15N analyses, 15N tracer methods, and a model of protein metabolism it is shown that the nitrogen balance is a useful concept for expressing the relationship between the overall nitrogen intake of the body and the nitrogen excretion. After admistering low doses of 15N-labelled substances like protein and amino acids, the kinetics of digestion and absorption can be followed by measuring the 15N abundance in serum and urine of patients. A significant delay in the nitrogen absorption indicates gastrointestinal disorders

  18. Studies with 15N-lysine in colostomized hens. 1

    0.2% L-lysine with an atom-% 15N excess (15N') of 48% were given per day through a throat probe to three colostomized laying hybrids in addition to a pelleted ration of 120 g per animal and day. In the following 4 days unlabelled L-lysine was given. As the labelled lysine was given three times a day, the development of 15N' excretion could be pursued. 80 minutes after the 15N'-lysine dose a distinct atom-% 15N' could be detected in urine. 6 hours after the 15N' application 2.9%, 4.2% and 2.7%, resp. of the applied 15N' amount in urine were found. 8 days after the beginning of the experiment the excretion of 15N' in urine was 17.5% on the average of the consumed 15N' amount. 44% of the nitrogen in the ration, however, was excreted in urine. The results show that the lysine N is excreted to a considerably lower extent in urine than the nitrogen in the remaining ration. (author)

  19. 15N-ammonium test in clinical research

    By use of the 15N-ammonium test the liver function is investigated under influence of hormonal contraceptives in women and in liver diseases in children. With the described noninvasive nonradioactive isotope test the ammonia detoxification capability and the urea synthesis capacity of the liver is determined by measuring of the 15N excretion in ammonia and urea in urine after oral administering of 15N-ammonium chloride. The 15N-ammonium test shows a significant influence of the hormonal contraceptives on the liver function and gives diagnostic evidence for liver diseases in children. (author)

  20. 15N balance in wheat-moong-soybean cropping sequence

    Field experiments were conducted to study the effect of FYM and S on fertilizer 15N balance in wheat-moong-soybean cropping sequence, with the main emphasis on partial substitution of chemical fertilizer N through FYM. Response to partial substitution of N was observed in the first crop of the sequence. FYM substitution at higher level (50%) resulted in reduction of wheat yield, but 25% substitution of recommended N through FYM increased wheat yield. Total fertilizer N recovery by three crops wheat, moong and soybean grown in sequence ranged between 39 to 55 per cent of which 35 to 41 per cent was utilized by the first crop and 4 to 14 per cent by the second and third crops together while 21 to 36 per cent of the fertilizer N applied to wheat was present in soil after growing three crops. Fertilizer N recovery in soil plant system was 61 to 91 per cent. Higher fertilizer N recovery was associated with higher rate of substitution of FYM for chemical fertilizer. FYM boosted fertilizer N recovery and higher soil retentivity. Sulphur application had no significant effect on per cent residual fertilizer N retention in soil. (author)

  1. Studies with 15N-lysine in colostomized hens. 6

    3 colostomized laying hybrides received 91.40 mg L-lysine-15N-excess (15N') each over a period of 4 days in a metabolism experiment with 15N-lysine. After another 4 days, during which the hens received the same rations supplemented by commercial L-lysine, the animals were butchered and divided into individual fractions. After hydrochloric hydrolysis of organs and tissues the heavy nitrogen of lysine, histidine and arginine were separated, quantitatively evaluated, processed and measured with an emission spectrometer. Atom-% 15N' on an average amounted to 0.20 in the liver, 0.16 in the kidneys, 0.06 in the flesh and 0.05 in the bones. Of the rediscovered 15N' applied, feces contained 8.1 %, urine 18.3 %, the eggs 24.3 %, the blood 4.9 %, the flesh 20.5 %, the bones 5.2 %, the gastrointestinal tract with its contents 4.5 %, the liver 3.5 %, the kidneys 0.9 %, the reproductive organs 3.7 %, and the rest 6.1 %. The quota of rediscovery of the 15N' applied was 95.7 %. 62 % of the total 15N' was rediscovered in eggs, body and feces as lysine 15N'. There was significantly more 15N' in all arginine fractions than in histidine. The quota of the lysine-15N' of the total 15N' differed considerably in the fractions: < 40 % bones and blood; 48-56 % gastrointestinal tract, feces, oviduct, kidneys; 62-63 % remaining ovary, rest; 69-71 % eggs, flesh, liver. It could be proved that the α-amino group of lysine is to a large extent incorporated into other amino acids. Further proof that the amino acid metabolism proceeds in two phases was submitted, i.e. higher amounts of amino acids previously deposited in the body are used for egg synthesis. (author)

  2. Comparison of {sup 15}N- and {sup 13}C-determined parameters of mobility in melittin

    Zhu Lingyang [University Indianapolis, Department of Physics, Indiana University Purdue (United States); Prendergast, Franklyn G. [Mayo Foundation, Department of Pharmacology (United States); Kemple, Marvin D. [University Indianapolis, Department of Physics, Indiana University Purdue (United States)

    1998-07-15

    Backbone and tryptophan side-chain mobilities in the 26-residue, cytolytic peptide melittin (MLT) were investigated by {sup 15}N and {sup 13}C NMR. Specifically, inverse-detected {sup 15}N T{sub 1} and steady-state NOE measurements were made at 30 and 51 MHz on MLT at 22 deg. C enriched with {sup 15}N at six amide positions and in the Trp{sup 19} side chain. Both the disordered MLT monomer (1.2 mM peptide at pH 3.6 in neat water) and {alpha}-helical MLT tetramer (4.0 mM peptide at pH 5.2 in 150 mM phosphate buffer) were examined. The relaxation data were analyzed in terms of the Lipari and Szabo model-free formalism with three parameters: {tau}{sub m}, the correlation time for the overall rotation; S{sup 2}, a site-specific order parameter which is a measure of the amplitude of the internal motion; and {tau}{sub e}, a local, effective correlation time of the internal motion. A comparison was made of motional parameters from the {sup 15}N measurements and from {sup 13}C measurements on MLT, the latter having been made here and previously [Kemple et al. (1997) Biochemistry, 36, 1678-1688]. {tau}{sub m} and {tau}{sub e} values were consistent from data on the two nuclei. In the MLT monomer, S{sup 2} values for the backbone N-H and C{alpha}-H vectors in the same residue were similar in value but in the tetramer the N-H order parameters were about 0.2 units larger than the C{alpha}-H order parameters. The Trp side-chain N-H and C-H order parameters, and {tau}{sub e} values were generally similar in both the monomer and tetramer. Implications of these results regarding the dynamics of MLT are examined.

  3. Multinuclear NMR of 15 N labelled organic molecules

    The paper presents the application of multinuclear NMR techniques to the study of 15 N labeled organic molecules. There are some important points of great interest in such type of research, namely, structure determination, i.e. location of the 15 N in molecule and determination of 15 N concentration in order to obtain quantitative results about the intramolecular short and long range interaction. Different NMR techniques were used in the study of 13 C, 1 H and 15 N. Obtaining the 15 N NMR signal imposes some special preparation of the spectrometer. First, we had to manage a very large spectral window (-400 to +1200 ppm) which makes difficult finding the signal. Secondly, in the condition of proton decoupling, in a very large band, a decrease of the signal can occur due to the NOE negative effect. To avoid this effect, other decoupling method, called 'inverse gated 1 H decoupling' was used. As a reference, for 15 N, we used CH3NO2, fixed at 0 ppm. In order to find the suitable spectral window we used the formamide (15 N). The results of obtaining the 15 N-labeled procaine are presented. (author)

  4. Highly automated protein backbone resonance assignment within a few hours: the strategy and software package

    Sequential resonance assignment represents an essential step towards the investigation of protein structure, dynamics, and interaction surfaces. Although the experimental sensitivity has significantly increased in recent years, with the availability of high field magnets and cryogenically cooled probes, resonance assignment, even of small globular proteins, still generally requires several days of data collection and analysis using standard protocols. Here we introduce the BATCH strategy for fast and highly automated backbone resonance assignment of 13C, 15N-labelled proteins. BATCH makes use of the fast data acquisition and analysis tools BEST, ASCOM, COBRA, and HADAMAC, recently developed in our laboratory. An improved Hadamard encoding scheme, presented here, further increases the performance of the HADAMAC experiment. A new software platform, interfaced to the NMRView software package, has been developed that enables highly automated NMR data processing and analysis, sequential resonance assignment, and 13C chemical shift extraction. We demonstrate for four small globular proteins that sequential resonance assignment can be routinely obtained within a few hours, or less, in a highly automated and robust way

  5. 15N Fractionation in Star-Forming Regions and Solar System Objects

    Wirstrom, Eva; Milam, Stefanie; Adande, GIlles; Charnley, Steven; Cordiner, Martin

    2015-01-01

    A central issue for understanding the formation and evolution of matter in the early Solar System is the relationship between the chemical composition of star-forming interstellar clouds and that of primitive Solar System materials. The pristinemolecular content of comets, interplanetary dust particles and carbonaceous chondrites show significant bulk nitrogen isotopic fractionation relative to the solar value, 14N15N 440. In addition, high spatial resolution measurements in primitive materials locally show even more extreme enhancements of 14N15N 100.

  6. 15N2 incorporation and acetylene reduction by azospirillum isolated from rice roots and soils

    Nitrogen fixation by strains of Azospirillum isolated from several rice soils and rice cultivars was investigated by 15N2 incorporation and C2H2 reduction. C2H2 reducing ability markedly varied among the strains obtained from soils differing widely in their physico-chemical properties. Large variations in 15N2 incorporation by Azospirillum isolated from the roots of several rice cultivars were also noticed. The present study reveals that rice cultivars harbour Azospirillum with differential N2-fixing ability and that plant genotype is of importance for optimal associations. (orig.)

  7. 1H, 15N and 13C NMR resonance assignment, secondary structure and global fold of the FMN-binding domain of human cytochrome P450

    The FMN-binding domain of human NADPH-cytochrome P450 reductase,corresponding to exons 3-;7, has been expressed at high level in an active form and labelled with 13C and 15N. Most of the backbone and aliphatic side-chain 1H, 15Nand 13C resonances have been assigned using heteronuclear double- and triple-resonance methods, together with a semiautomatic assignment strategy. The secondary structure as estimated from the chemical shift index and NOE connectivities consists of six α-helices and fiveβ-strands. The global fold was deduced from the long-range NOE sun ambiguously assigned in a 4D 13C-resolved HMQC-NOESY-HMQC spectrum. The fold is of the alternating α/β type, with the fiveβ-strands arranged into a parallel β-sheet. The secondary structure and global fold are very similar to those of the bacterial flavodoxins, but the FMN-binding domain has an extra short helix in place of a loop, and an extra helix at the N-terminus (leading to the membrane anchordomain in the intact P450 reductase). The experimental constraints were combined with homology modelling to obtain a structure of the FMN-bindingdomain satisfying the observed NOE constraints. Chemical shift comparisons showed that the effects of FMN binding and of FMN reduction are largely localised at the binding site

  8. A direct electrifying algorithm for backbone identification

    This paper proposes a new algorithm for identifying backbones in the application of percolation theory. This algorithm is based on the current-carrying definition of backbone and is carried out on the predetermined spanning cluster. It is fairly easy to implement and further parallelize. The efficiency is enhanced by the fact that the conductivity of a percolating system can be obtained in the same processing of backbone identification. The critical exponents of backbone mass, red bonds (sites) and conductivity obtained by this algorithm are in very good agreement with the existing results

  9. 3D-TROSY-based backbone and ILV-methyl resonance assignments of a 319-residue homodimer from a single protein sample

    Krejcirikova, Anna; Tugarinov, Vitali, E-mail: vitali@umd.edu [University of Maryland, Department of Chemistry and Biochemistry (United States)

    2012-10-15

    The feasibility of practically complete backbone and ILV methyl chemical shift assignments from a single [U-{sup 2}H,{sup 15}N,{sup 13}C; Ile{delta}1-{l_brace}{sup 13}CH{sub 3}{r_brace}; Leu,Val-{l_brace}{sup 13}CH{sub 3}/{sup 12}CD{sub 3}{r_brace}]-labeled protein sample of the truncated form of ligand-free Bst-Tyrosyl tRNA Synthetase (Bst-{Delta}YRS), a 319-residue predominantly helical homodimer, is established. Protonation of ILV residues at methyl positions does not appreciably detract from the quality of TROSY triple resonance data. The assignments are performed at 40 Degree-Sign C to improve the sensitivity of the measurements and alleviate the overlap of {sup 1}H-{sup 15}N correlations in the abundant {alpha}-helical segments of the protein. A number of auxiliary approaches are used to assist in the assignment process: (1) selection of {sup 1}H-{sup 15}N amide correlations of certain residue types (Ala, Thr/Ser) that simplifies 2D {sup 1}H-{sup 15}N TROSY spectra, (2) straightforward identification of ILV residue types from the methyl-detected 'out-and-back' HMCM(CG)CBCA experiment, and (3) strong sequential HN-HN NOE connectivities in the helical regions. The two subunits of Bst-YRS were predicted earlier to exist in two different conformations in the absence of ligands. In agreement with our earlier findings (Godoy-Ruiz in J Am Chem Soc 133:19578-195781, 2011), no evidence of dimer asymmetry has been observed in either amide- or methyl-detected experiments.

  10. Application of 15N in biochemistry, agriculture and medicine

    The compendium on application of 15N in the biosciences comprises 7 chapters. The 1st chapter comprehends introductory remarks on isotopes in general and on nitrogen isotopes in particular. In the 2nd chapter fundamentals of 15N tracer techniques are discussed. The 3rd chapter deals with experiment programs and the evaluation of experiments. The methodology of sample preparation as well as of isotope analysis is treated in chapter 4. The chapters 5 to 7 deal with the application of 15N as tracer in biochemistry, agricultural research and medicine, resp. Relevant literature is added to each chapter

  11. Struktur- und Bindungsuntersuchungen nichtextrahierbarer 15 N- und 14 C-Simazinrückstände im Boden

    Berns, Anne Elisabeth

    2003-01-01

    The aim of the presented study was the characterization of the structure and binding modes of non-extractable residues (NER) of the triazine herbicide simazine. The chemical environments of unaltered as well as metabolized simazine compounds can be observed directly in soil or compost matrix by 15N-NMR spectroscopy. As the 15N-isotope has a very low sensitivity and natural abundance 15N-labeled simazine was used. To further enhance the signal to noise ratio and sensitivity of the NMR experime...

  12. 1H, 13C, and 15N resonance assignment of the ubiquitin-like domain from Dsk2p

    Chen, Tony; Zhang, Daoning; Matiuhin, Yulia; Glickman, Michael; Fushman, David

    2008-01-01

    The ubiquitin-like domain (UBL) of yeast protein Dsk2p is widely believed to recognize and bind to ubiquitin receptors on the proteasome and, as part of Dsk2p, to bridge polyubiquitinated substrates and proteasomal degradation machinery. Here we report NMR resonance assignment for 1H, 15N, and 13C nuclei in the backbone and side chains of the UBL domain of Dsk2p. This assignment will aid in NMR studies focused on understanding of Dsk2’s interactions with proteasomal receptors and its role as ...

  13. Reduced Dimensionality tailored HN(C)N Pulse Sequences for Efficient Backbone Resonance Assignment of Proteins through Rapid Identification of Sequential HSQC peaks

    Kumar, Dinesh

    2013-01-01

    Two novel reduced dimensionality (RD) experiments -(4,3)D-hNCOcaNH and (4,3)D-hNcoCANH- have been presented here to facilitate the backbone resonance assignment of proteins both in terms of its accuracy and speed. The experiments basically represent an improvisation of previously reported HN(C)N experiment [Panchal et. al., J. Biomol. NMR. (2002), 20 (2), 135-147] and exploit the simple reduced dimensionality NMR concept [Szyperski et. al. (2002), Proc. Natl. Acad. Sci. U.S.A. 99(12), 8009-8014] to achieve (a) higher dispersion and resolution along the co-evolved F1 dimension and (b) rapid identification of sequential HSQC peaks on its F2(15N)- F3(1H) planes. The current implementation is based on the fact that the linear combination of 15N and 13CO/13Ca chemical shifts offers relatively better dispersion and randomness compared to the individual chemical shifts; thus enables the assignment of crowded HSQC spectra by resolving the ambiguities generally encountered in HNCN based assignment protocol because of ...

  14. Stereospecific assignments of glycine in proteins by stereospecific deuteration and {sup 15}N labeling

    Hansen, A.P.; Curley, R.W. Jr.; Panigot, M.J.; Fesik, S.W. [Ohio State Univ., Columbus, OH (United States)

    1994-12-01

    Stereospecific assignments are important for accurately determining the three-dimensional structures of proteins through the use of multidimensional NMR techniques. It is especially important to stereospecifically assign the glycine {alpha}-protons in proteins because of the potential for different backbone conformations of this residue. These stereospecific assignments are critical for interpreting the {sup 3}J{sub NH,{alpha}H} coupling constants and NOEs involving the glycine {alpha}-protons that determine the conformation of this part of the protein. However, it is often difficult to unambiguously obtain the stereospecific assignments for glycine residues by using only NOE data. In this poster, we present a method for unambiguous, stereospecific assignment of the {alpha}-protons of glycine residues. This method involves synthesis of stereo-specifically deuterated and {sup 15}N-labeled Gly using a slightly modified procedure originally described by Woodard and coworkers for the stereoselective deuteration of glycine. The stereospecifically deuterated and {sup 15}N-labeled Gy has been incorporated into recombinant proteins expressed in both bacterial systems (FKBP) and mammalian cells (u-PA). Two- and three-dimensional isotope-filtered and isotope-edited NMR experiments were used to obtain the stereospecific assignments of the glycine {alpha}-protons for these proteins.

  15. The absorption, utilization and distribution of nitrate 15N and ammonium 15N in Populus Tomentosa seedlings

    Effects of different nitrogen sources (NO3-, NH4+) on the absorption, distribution and utilization of nitrogen on Populus tenement's seedlings (clone 50) was studied by using the 15N trace technique. Results showed that the Populus tenement's seedlings had the same nitrogen take up pattern: tissue nitrogen content grew up after fertilization, remarkbaly rising up after one week and reached peak after 28 days. Although the treatments are different, the tissue N content was about the same between 0.6g · plant-1. The maximum absorption of NO3-15N and NH4-15N was 0.26g · plant-1 and 0.12g · plant -1, which accounted for 39.15% and 19.95% of total nitrogen, respectively. The nitrogen use efficiency (NUE) of two nitrogen sources varied gignificantly. The maximum NUE of NO3-15N reached 25.83%, nearly twice of that of NH4-15N (12.03%). Hence we conclude that Populus tomentosa seedlings (clone 50) prefer to absorb NO3-. Nitrogen distribution rate changed obviously among different organs and the trend was leaf>root>stem. In the leaf, the distribution of NO3-15N was higher than that of NH4-15N. (authors)

  16. Monitoring the refinement of crystal structures with 15N solid-state NMR shift tensor data

    The 15N chemical shift tensor is shown to be extremely sensitive to lattice structure and a powerful metric for monitoring density functional theory refinements of crystal structures. These refinements include lattice effects and are applied here to five crystal structures. All structures improve based on a better agreement between experimental and calculated 15N tensors, with an average improvement of 47.0 ppm. Structural improvement is further indicated by a decrease in forces on the atoms by 2–3 orders of magnitude and a greater similarity in atom positions to neutron diffraction structures. These refinements change bond lengths by more than the diffraction errors including adjustments to X–Y and X–H bonds (X, Y = C, N, and O) of 0.028 ± 0.002 Å and 0.144 ± 0.036 Å, respectively. The acquisition of 15N tensors at natural abundance is challenging and this limitation is overcome by improved 1H decoupling in the FIREMAT method. This decoupling dramatically narrows linewidths, improves signal-to-noise by up to 317%, and significantly improves the accuracy of measured tensors. A total of 39 tensors are measured with shifts distributed over a range of more than 400 ppm. Overall, experimental 15N tensors are at least 5 times more sensitive to crystal structure than 13C tensors due to nitrogen’s greater polarizability and larger range of chemical shifts

  17. Green Network Planning Model for Optical Backbones

    Gutierrez Lopez, Jose Manuel; Riaz, M. Tahir; Jensen, Michael;

    2010-01-01

    Communication networks are becoming more essential for our daily lives and critically important for industry and governments. The intense growth in the backbone traffic implies an increment of the power demands of the transmission systems. This power usage might have a significant negative effect...... an analytical model to consider environmental aspects in the planning stage of backbones design....

  18. Study on synthesis of 15N-hydrazine hydrate

    The 15N labeled hydrazine hydrate is a strong reducing agent in the synthesis procedure of stable isotope labeled compounds, and it has been widely used in the isotope-labeled pharmaceutical synthesis. The reaction conditions of 15N labeled hydrazine hydrate were mainly investigated by single-factor design, and the following optimized conditions were obtained: the concentration of available chlorine was 115-120 g/L, the chlorination re- action time was 30∼40 min, the reflux time was 7 min, and the mass ratio of material was m(catalyst) : m (urea) = 1.0 : 10.0, and the yield of 15N labeled hydrazine hydrate was 76.1%, the abundance of 15N was 99.20%. (authors)

  19. Studies with 15N-Lysine in colostomized hens. 4

    Each of 3 colostomized laying hens received per os 0.2% L-lysine with 48 atom-% 15N excess (15N') labelled in α-position in addition to a pelleted laying hen ration of 120 g over a period of 4 days. On the following 4 days they received equal amounts of unlabelled lysine. The eggs laid during the 8 days of the experiment were separated into the egg white, the yolk and the eggshell, and the total and heavy nitrogen in the individual fractions were determined. Above that, 17 amino acids and their atom-%15N' were determined in the 19 samples of the white and yolk of egg. Of the total 15N' from the lysine fed in the 4 days, 10.1% were found in the yolk, 10.5% in the egg white and 1.1% in the eggshells of the eggs laid during the 8 days of the experiment. 85% of the total amino acid 15N' of the yolk and 86% of the egg white detected to be lysine 15N'. The 15N' amount of the other 16 amino acids was mainly concentrated in the two acid and basic amino acids. Approximately 50% of the non-lysine 15N' in the egg are contained in aspartic acid, glutamic acid, histidine and arginine. A very low incorporation of the labelled lysine only could be detected in the aromatic and sulphur-containing amino acids from both the yolk and the egg white 43% of the 15N' was detected in the 10 essential and semi-essential (except lysine) and 57% in the 6 non-essential amino acids of the yolk and 52% and 48% resp. of the egg white. One can summarise that the incorporation of 15N' into the egg shows the same development as that of the labelled amino acids of the wheat protein and that 15% of the lysine 15N' could be detected in the 16 other amino acids. (author)

  20. Protein-Backbone Thermodynamics across the Membrane Interface.

    Bereau, Tristan; Kremer, Kurt

    2016-07-01

    The thermodynamics of insertion of a protein in a membrane depends on the fine interplay between backbone and side-chain contributions interacting with the lipid environment. Using computer simulations, we probe how different descriptions of the backbone glycyl unit affect the thermodynamics of insertion of individual residues, dipeptides, and entire transmembrane helices. Due to the lack of reference data, we first introduce an efficient methodology to estimate atomistic potential of mean force (PMF) curves from a series of representative and uncorrelated coarse-grained (CG) snapshots. We find strong discrepancies between two CG models, Martini and PLUM, against reference atomistic PMFs and experiments. Atomistic simulations suggest a weak free energy of insertion between water and a POPC membrane for the glycyl unit, in overall agreement with experimental results despite severe assumptions in our calculations. We show that refining the backbone contribution in PLUM significantly improves the PMF of insertion of the WALP16 transmembrane peptide. An improper balance between the glycyl backbone and the attached side chain will lead to energetic artifacts, rationalizing Martini's overstabilization of WALP's adsorbed interfacial state. It illustrates difficulties associated with free-energy-based parametrizations of single-residue models, as the relevant free energy of partitioning used for force-field parametrization does not arise from the entire residue but rather the solvent-accessible chemical groups. PMID:27138459

  1. Balance study of the fate of 15N fertilizer

    An interim report is presented on a series of experiments with wooden box-type lysimeters (60 cm x 60 cm x 70 cm) loaded with a sandy soil, a loess soil and straw-amended soil. The lysimeters support crops rotated over a five-year period to be studied - potato, barley, sugar-beet, barley (with winter rape) and finally (1979) potato. Each lysimeter received split applications of urea at total rates of 0, 50 or 100 kg.ha-1. The effects of soil residues of the herbicide monolinuron were also studied. The report deals with data collected during the first three years of the planned experiments (1975 - 1977 inclusive). 15N-labelled urea (47 atom 15N% excess) was initially used but in some experiments this was followed by applications of unlabelled urea in order to study the fate of the residual 15N in the subsequent years. The results to date indicated that in the first year highest recoveries in the plant of the applied 15N obtained on the sandy soil. The low recoveries of 15N in the subsequent years when unlabelled urea was supplied also indicated significant storage by soil or root organic matter of the applied 15N. Compared with the control (zero application of urea nitrogen), potato took up more total nitrogen in the presence of fertilizer including more of the unlabelled soil pool nitrogen. Analyses of the soil profiles in terms of total soil nitrogen and fertilizer-derived nitrogen (on the basis of 15N assays) indicated leaching of the labelled nitrogen down the soil profile in all cases during the three-year period. Analysis of NO3-N in leachates confirmed the presence of labelled urea-derived nitrogen. (author)

  2. Effects of compost application on fruits yields, sugar and mineral contents and δ15N values of tomato fruits

    We examined the effects of chemical fertilizer and compost application on the yields and sugar and mineral content of tomato (Lycopersicon esculentum Mill. Saturn) in an isolated bed. Five treatments were conducted within a two-year period of 4 continuous croppings. CDU and LSR (Low-sulfate slow-release fertilizer) were used for the chemical fertilizer plots. A mixture of cattle manure and CDU (CM + CDU), a mixture of poultry manure and CDU (PM + CDU), and mixture of cattle and poultry manure (PM + CM) plots were arranged as compost-using plots. We also measured the δ15N values of tomatoes and the soils of each treatment, and estimated the correlation of the δ15N values between fruits and soil to certify compost applied products. We did not find any reproductive differences in the yield or sugar content among the treatments. As to inorganic content of tomatoes, there were no significant differences except for Mg content among the plots. These results showed that it is difficult to assay regular benefit of organic fertilizer application to tomato yields and quality. On the other hand, δ15N values of tomato fruits showed significant differences among fertilizer applications. δ15N values of the chemical fertilizer were +1.6 per mille and -1.1% for CDU and LSR, respectively. Those of mixture of chemical and compost were +12.2 per mille and +11.2 per mille for CM + CDU and PM + CDU, respectively. The mixture of PM and CM showed the highest δ15N values (17.9 per mille) among the treatments. δ15N values of the soils and fruits reflected those of the fertilizers and were positively correlated (R2 = 0.89). It may be possible to use δ15N values as an indicator of organic products by setting the threshold point, e.g. +5.0 per mille, to distinguish them from the products cultivated with chemical fertilizer. (author)

  3. ~(15)N Isotope Used for Study of Groundwater Nitrogen Pollution in Shijiazhuang City, China

    2004-01-01

    Shijiazhuang City is the capital of Hebei province, China. Groundwater is the major water supply source for living and industry need of the city. Due to a rapid increase of population and development of industry and agriculture, a series of groundwater environmental problems are created. In the paper, the situation of groundwater pollution in Shijiazhuang city is reported. Based on the groundwater chemical data and ~(15)N measurement results both on groundwater and soils, the reason of groundwater nitra...

  4. Utilization of 15N-urea in laying hens. 3

    In 3 colostomized laying hens the incorporation of heavy nitrogen from urea into the amino acids of the 21 eggs laid during the 8-day experiment was determined. In these eggs the content of 15 amino acids was ascertained separately in white and yolk of the eggs and their atom-% 15N excess (15N') was determined. The heavy nitrogen could be detected in all amino acids investigated. The incorporation of 15N' into the essential amino acids of the white and yolk of eggs is very low. Of the 15N' amount of the urea applied 0.18% could be detected in the 9 essential amino acids of the white of egg and 0.12% in those of the yolk. For the 6 analyzed nonessential amino acids the rediscovery quota of 15N' in the white of egg was 0.50% and in the yolk 0.81% is that the NPN-source urea is insignificant for egg protein synthesis. (author)

  5. Ner protein of phage Mu: Assignments using {sup 13}C/{sup 15}N-labeled protein

    Strzelecka, T.; Gronenborn, A.M.; Clore, G.M. [National Institutes of Health, Bethesda, MD (United States)

    1994-12-01

    The Ner protein is a small (74-amino acid) DNA-binding protein that regulates a switch between the lysogenic and lytic stages of phage Mu. It inhibits expression of the C repressor gene and down-regulates its own expression. Two-dimensional NMR experiments on uniformly {sup 15}N-labeled protein provided most of the backbone and some of the sidechain proton assignments. The secondary structure determination using two-dimensional NOESY experiments showed that Ner consists of five {alpha}-helices. However, because most of the sidechain protons could not be assigned, the full structure was not determined. Using uniformly {sup 13}C/{sup 15}N-labeled Ner and a set of three-dimensional experiments, we were able to assign all of the backbone and 98% of the sidechain protons. In particular, the CBCANH and CBCA(CO)NH experiments were used to sequentially assign the C{alpha} and C{beta} resonances; the HCCH-CTOCSY and HCCH-COSY were used to assign sidechain carbon and proton resonances.

  6. Exercise: The Backbone of Spine Treatment

    Full Text Available Exercise: The Backbone of Spine Treatment | View Video Back Purchase Video Struggling with Low Back Pain? Many people are surprised to learn that carefully selected exercise can ...

  7. Exercise: The Backbone of Spine Treatment

    Exercise: The Backbone of Spine Treatment | View Video Back Purchase Video Struggling with Low Back Pain? Many people are surprised to learn that carefully selected exercise can actually reduce back pain. Some exercises can ...

  8. Exercise: The Backbone of Spine Treatment

    Full Text Available Exercise: The Backbone of Spine Treatment | View Video Back Purchase Video Struggling with Low Back Pain? Many people are surprised to learn that carefully selected exercise can actually reduce back pain. Some exercises can ...

  9. Comparison of the backbone dynamics of wild-type Hydrogenobacter thermophilus cytochrome c{sub 552} and its b-type variant

    Tozawa, Kaeko; Ferguson, Stuart J.; Redfield, Christina, E-mail: christina.redfield@bioch.ox.ac.uk [University of Oxford, Department of Biochemistry (United Kingdom); Smith, Lorna J., E-mail: lorna.smith@chem.ox.ac.uk [University of Oxford, Department of Chemistry (United Kingdom)

    2015-06-15

    Cytochrome c{sub 552} from the thermophilic bacterium Hydrogenobacter thermophilus is a typical c-type cytochrome which binds heme covalently via two thioether bonds between the two heme vinyl groups and two cysteine thiol groups in a CXXCH sequence motif. This protein was converted to a b-type cytochrome by substitution of the two cysteine residues by alanines (Tomlinson and Ferguson in Proc Natl Acad Sci USA 97:5156–5160, 2000a). To probe the significance of the covalent attachment of the heme in the c-type protein, {sup 15}N relaxation and hydrogen exchange studies have been performed for the wild-type and b-type proteins. The two variants share very similar backbone dynamic properties, both proteins showing high {sup 15}N order parameters in the four main helices, with reduced values in an exposed loop region (residues 18–21), and at the C-terminal residue Lys80. Some subtle changes in chemical shift and hydrogen exchange protection are seen between the wild-type and b-type variant proteins, not only for residues at and neighbouring the mutation sites, but also for some residues in the heme binding pocket. Overall, the results suggest that the main role of the covalent linkages between the heme group and the protein chain must be to increase the stability of the protein.

  10. 15N-labelled pyrazines of triterpenic acids

    Triterpenoid pyrazines from our research group were found selectively cytotoxic on several cancer cell lines with IC50 in low micromolar range. This sparked our interest in preparing their labeled analogs for metabolic studies. In this work, we prepared a set of non-labeled pyrazines from seven triterpenoid skeletal types along with their 15N labelled analogs. In this work, we present the synthesis and characterization of the target 15N labelled pyrazines. Currently, these compounds are being studied in complex metabolic studies. (author)

  11. The 15N ground state studied with elastic electron scattering

    The C0 elastic electron scattering form factor of 15N has been measured over a momentum transfer range q = 0.4-3.2 fm-1. From these form factor data the ground state charge density and its RMS radius (2.612±0.009 fm) were determined. This charge density as well as its difference with that of 16O were compared to recent large-basis shell-model calculations. Although these calculations describe the individual charge density reasonably, the difference between 16O and 15N cannot be reproduced satisfactorily. (orig.)

  12. 15N magnetic resonance of aqueous imidazole and zinc(II)-imidazole complexes. Evidence for hexacoordination

    15N NMR chemical shifts of doubly labeled [15N)imidazole permit evaluation of hydrogen bonding, proton association, and Zn(II) complex formation in homogeneous solution. The 15N resonant frequency in aqueous solutions of imidazole at pH 9-12 is independent of imidazole concentration, suggesting insignificant self-association via hydrogen bonding involving the N3 lone pair and the N1 proton of a neighboring molecule. Protonation at N3 (pH less than 5) produces a 31.2-ppM diamagnetic shift and deprotonation at N1 (pH greater than 13) an approximately20-ppM paramagnetic shift relative to neutral aqueous imidazole. Those shifts are very large compared to the approximately +-0.5-ppM uncertainty in the 15N shift measurements. In solutions of Zn2+ and imidazole the 15N resonance in ZnIm/sub i/2+ complexes (Im = imidazole) is diamagnetically shifted by 10 to 20 ppM relative to neutral aqueous imidazole. Over a range of ratios of total imidazole to total zinc such that the average number of complexed imidazole molecules per Zn2+ (anti ν) is approximately 3.5, or less, the shift data are well interpreted by a four-species model (i = 1-4) using stepwise formation constants from the literature. Significant deviations from that model at anti ν greater than 3.5 require that higher species (e.g., ZnIm52+ and ZnIm62+) be considered. A six-species model with reasonable formation constants for the fifth and sixth complexes provides satisfactory interpretation of all data. Implications of those observations with respect to biologically active zinc(II) proteins are considered. 2 tables, 4 figures

  13. 15N Solid-State NMR as a Probe of Flavin H-bonding

    Cui, Dongtao; Koder, Ronald L.; Dutton, P. Leslie; Miller, Anne-Frances

    2011-01-01

    Flavins mediate a wide variety of different chemical reactions in biology. To learn how one cofactor can be made to execute different reactions in different enzymes, we are developing solid-state NMR (SSNMR) to probe the flavin electronic structure, via the 15N chemical shift tensor principal values (δii). We find that SSNMR has superior responsiveness to H-bonds, compared to solution NMR. H-bonding to a model of the flavodoxin active site produced an increase of 10 ppm in the δ11 of N5 altho...

  14. Detection of organic sulfur by [sup 15]N and [sup 19]F NMR via formation of iminosulfuranes

    Franz, J.A.; Linehan, J.C.; Lamb, C.N.

    1992-08-01

    We have synthesized new iminosulfuranes from a variety of diaryl-and dialkyl sulfides and dibenzothiophene. The pattern of [sup 15]N chemical shifts indicates that functional groups attached to sulfur are not simply resolved into aryl and alkyl groups. Thus, resolution of sulfur functional groups using [sup 15]N NMR via iminosulfurane does not appear practicable. However, iminosulfurane formation, together with the N-haloamide reaction and the Pummerer rearrangement, provides pathways for chemical discrimination of different sulfur substituents using unique [sup 15]N- or, [sup 19]F-labelled fragments for different categories of sulfur functional groups. In efforts currently underway, we are applying these reactions to methylated extracts and conversion products of the high-organic-sulfur containing Yugoslavian Rasa and Spanish Mequinenza lignites. 1 tab, 14 refs.

  15. Detection of organic sulfur by {sup 15}N and {sup 19}F NMR via formation of iminosulfuranes

    Franz, J.A.; Linehan, J.C.; Lamb, C.N.

    1992-08-01

    We have synthesized new iminosulfuranes from a variety of diaryl-and dialkyl sulfides and dibenzothiophene. The pattern of {sup 15}N chemical shifts indicates that functional groups attached to sulfur are not simply resolved into aryl and alkyl groups. Thus, resolution of sulfur functional groups using {sup 15}N NMR via iminosulfurane does not appear practicable. However, iminosulfurane formation, together with the N-haloamide reaction and the Pummerer rearrangement, provides pathways for chemical discrimination of different sulfur substituents using unique {sup 15}N- or, {sup 19}F-labelled fragments for different categories of sulfur functional groups. In efforts currently underway, we are applying these reactions to methylated extracts and conversion products of the high-organic-sulfur containing Yugoslavian Rasa and Spanish Mequinenza lignites. 1 tab, 14 refs.

  16. Sequence-specific assignment of histidine and tryptophan ring 1H, 13C and 15N resonances in 13C/15N- and 2H/13C/15N-labelled proteins

    Methods are described to correlate aromatic 1Hδ2/13Cδ2 or 1Hε1/15Nε1 with aliphatic 13Cβ chemical shifts of histidine and tryptophan residues, respectively. The pulse sequences exclusively rely on magnetization transfers via one-bond scalar couplings and employ [15N, 1H]- and/or [13C, 1H]-TROSY schemes to enhance sensitivity. In the case of histidine imidazole rings exhibiting slow HN-exchange with the solvent, connectivities of these proton resonances with β-carbons can be established as well. In addition, their correlations to ring carbons can be detected in a simple [15N, 1H]-TROSY-H(N)Car experiment, revealing the tautomeric state of the neutral ring system. The novel methods are demonstrated with the 23-kDa protein xylanase and the 35-kDa protein diisopropylfluorophosphatase, providing nearly complete sequence-specific resonance assignments of their histidine δ-CH and tryptophan ε-NH groups

  17. Nitrogen input 15N-signatures are reflected in plant 15N natural abundances of N-rich tropical forest in China

    Abdisa Gurmesa, Geshere; Lu, Xiankai; Gundersen, Per; Yunting, Fang; Mo, Jiangming

    2016-04-01

    In this study, we tested the measurement of natural abundance of 15N15N) for its ability to assess changes in N cycling due to increased N deposition in two forest types; namely, an old-growth broadleaved forest and a pine forest, in southern China. We measured δ15N values of inorganic N in input and output fluxes under ambient N deposition, and N concentration and δ15N of major ecosystem compartments under ambient and increased N deposition. Our results showed that N deposition to the forests was 15N-depleted, and was dominated by NH4-N. Plants were 15N-depleted due to imprint from the 15N-depleted atmospheric N deposition. The old-growth forest had larger N concentration and was more 15N-enriched than the pine forest. Nitrogen addition did not significantly affect N concentration, but it significantly increased δ15N values of plants, and slightly more so in the pine forest, toward the 15N signature of the added N in both forests. The result indicates that the pine forest may rely more on the 15N-depleted deposition N. Soil δ15N values were slightly decreased by the N addition. Our result suggests that ecosystem δ15N is more sensitive to the changes in ecosystem N status and N cycling than N concentration in N-saturated sub-tropical forests.

  18. Isotopic enrichment of 15N by ionic exchange cromatography

    The ionic exchange chromatographic method in columns of resin which is employed in the study of isotopic enrichment of 15N is presented. Determinations are made of the isotopic separation constant for the exchange of isotopes 15N and 14N in the equilibrium involving ammonium hidroxide in the solution phase and ions NH4+ adsorbed in cationic resins: Dowex 50W-X8 and X12, 100-200 mesh. Experiments are also conducted for determination of height of theoretical plates for situations of equilibrium of the NH4+ band in two systems of resin's columns aimed at estimating the experimental conditions used. The isotopic analyses of nitrogen are carried out by mass spectrometry

  19. Marking Drosophila suzukii (Diptera: Drosophilidae) With Rubidium or 15N.

    Klick, J; Yang, W Q; Bruck, D J

    2015-06-01

    Drosophila suzukii Matsumura (Diptera: Drosophilidae) has caused significant economic damage to berry and stone fruit production regions. Markers that are systemic in plants and easily transferred to target organisms are needed to track D. suzukii exploitation of host resources and trophic interactions. High and low concentrations of the trace element, rubidium (Rb), and the stable isotope, 15N, were tested to mark D. suzukii larvae feeding on fruits of enriched strawberry plants grown in containers under greenhouse conditions. Fly marker content and proportion of flies marked 1, 7, and 14 d after emergence from enriched fruits and fly dry mass were analyzed. Nearly 100% of the flies analyzed 14 d after emerging from 15N-enriched plants were marked, whereas only 30-75% and 0-3% were marked 14 d after emerging from high and low Rb concentration plants, respectively. Rapid Rb decay, strong 15N persistence, and the economics of using these markers in the field to elucidate D. suzukii pest ecology are discussed. PMID:26470275

  20. Geomorphic control on the δ15N of mountain forests

    R. G. Hilton

    2013-03-01

    Full Text Available Mountain forests are subject to high rates of physical erosion which can export particulate nitrogen from ecosystems. However, the impact of geomorphic processes on nitrogen budgets remains poorly constrained. We have used the elemental and isotopic composition of soil and plant organic matter to investigate nitrogen cycling in the mountain forest of Taiwan, from 24 sites with distinct geomorphic (topographic slope and climatic (precipitation, temperature characteristics. The organic carbon to nitrogen ratio of soil organic matter decreased with soil 14C age, providing constraint on average rates of nitrogen loss using a mass balance model. Model predictions suggest that present day estimates of nitrogen deposition exceed contemporary and historic nitrogen losses. We found ∼6‰ variability in the stable isotopic composition (δ15N of soil and plants which was not related to soil 14C age or climatic conditions. Instead, δ15N was significantly, negatively correlated with topographic slope. Using the mass balance model, we demonstrate that the correlation can be explained by an increase in nitrogen loss by non-fractioning pathways on steeper slopes, where physical erosion most effectively removes particulate nitrogen. Published data from forests on steep slopes are consistent with the correlation. Based on our dataset and these observations, we hypothesise that variable physical erosion rates can significantly influence soil δ15N, and suggest particulate nitrogen export is a major, yet underappreciated, loss term in the nitrogen budget of mountain forests.

  1. Absorption of ammonium sulphate 15N by coffee plants

    The objective of this study was to quantify the absorption of ammonium sulphate 15N by coffee plants. Treatments consisted of five sub-plots of 9 plants, of which the three central ones received 280 kg ha-1 of 15N, applied at four times: 1/4 on 01 Set 03; 1/4 on 03 Nov 03; 1/4 on 15 Dec 03 and 1/4 on 30 Jan 04. The isotopic enrichment was 2,072 ± 0,001 atom % 15N. The dry matter of the shoot was evaluated every 60 days, using one plant per replicate, collected outside the sub-plot. They were as similar as possible to the labeled plants, which were used only for isotopic and Total N analysis, after being dried at 65 deg C until constant weight. At harvest, plants had absorbed 42,88% of the fertilizer N. Leaves accumulated the largest amount of fertilizer N, and were also the compartments that received most N from other parts of the plant. The following partition of the fertilizer N was found at harvest: 23.01% in young leaves, 6.23% in old leaves, 4,46% in stem, 3.46% in fruits, 3.10% in young branches and 2.63% in old branches. (author)

  2. COVALENT BINDING OF REDUCED METABOLITES OF [15N3] TNT TO SOIL ORGANIC MATTER DURING A BIOREMEDIATION PROCESS ANALYZED BY 15N NMR SPECTROSCOPY. (R826646)

    Evidence is presented for the covalent binding ofbiologically reduced metabolites of 2,4,6-15N3-trinitrotoluene(TNT) to different soil fractions (humic acids, fulvicacids, and humin) using liquid 15N NMR spectroscopy. Asilylation p...

  3. Variation of natural sup 15 N abundance of crops and soils in Japan with special reference to the effect of soil conditions and fertilizer application

    Yoneyama, Tadakatsu (National Agriculture Research Center, Tsukuba, Ibaraki (Japan). Dept. of Soils and Fertilizers); Kouno, Kazumi; Yazaki, Jinya

    1990-12-01

    The natural {sup 15}N abundance ({delta}{sup 15}N) of the crops subjected to long-term fertilizer treatments under paddy and upland conditions in the different experimental stations throughout Japan were analyzed. The {delta}{sup 15}N values of the grains of paddy rice which were +6.3 per mille on the average in the fields without application of chemical fertilizers decreased by the treatment with chemical fertilizers. The average {delta}{sup 15}N values of the upland crops were lower than those of paddy rice without application of N fertilizers. The {delta}{sup 15}N values of upland crops decreased with the dose of chemical fertilizer N, but increased with the application of composts containing animal feces. The pot experiments using three soils showed that the {delta}{sup 15}N values of paddy rice were higher than those of upland rice and sorghum and that these values were comparable to the {delta}{sup 15}N values of ammonium and nitrate produced in the incubated soils, respectively. The {delta}{sup 15}N values of fertilizer N absorbed by paddy rice were higher than those of fertilizer N, whereas the {delta}{sup 15}N values of the fertilizer N in upland rice and sorghum were increased in the alluvial soils but decreased in Andosols as compared to those of fertilizer N applied. The {delta}{sup 15}N values of the Andosols in Japan showed small variations, with an average value of +6.5 per mille, whereas those of alluvial soils in Japan showed large variations with an average value lower than that of Andosols. (author).

  4. Variation of natural 15N abundance of crops and soils in Japan with special reference to the effect of soil conditions and fertilizer application

    The natural 15N abundance (δ15N) of the crops subjected to long-term fertilizer treatments under paddy and upland conditions in the different experimental stations throughout Japan were analyzed. The δ15N values of the grains of paddy rice which were +6.3 per mille on the average in the fields without application of chemical fertilizers decreased by the treatment with chemical fertilizers. The average δ15N values of the upland crops were lower than those of paddy rice without application of N fertilizers. The δ15N values of upland crops decreased with the dose of chemical fertilizer N, but increased with the application of composts containing animal feces. The pot experiments using three soils showed that the δ15N values of paddy rice were higher than those of upland rice and sorghum and that these values were comparable to the δ15N values of ammonium and nitrate produced in the incubated soils, respectively. The δ15N values of fertilizer N absorbed by paddy rice were higher than those of fertilizer N, whereas the δ15N values of the fertilizer N in upland rice and sorghum were increased in the alluvial soils but decreased in Andosols as compared to those of fertilizer N applied. The δ15N values of the Andosols in Japan showed small variations, with an average value of +6.5 per mille, whereas those of alluvial soils in Japan showed large variations with an average value lower than that of Andosols. (author)

  5. A novel method for trapping and analyzing 15N in NO for tracing NO sources

    Kang, Ronghua; Mulder, Jan; Dörsch, Peter

    2016-04-01

    15N isotope tracing is an effective and direct approach to investigate the biological and chemical sources of nitric oxide (NO) in soil. However, NO is highly reactive and rapidly converted to nitrogen dioxide (NO2) in the presence of ozone. Various chemical conversions of NO to the more stable solutes nitrite (NO2-) and nitrate (NO3-) have been proposed, which allow analysing the 15N abundance without major fractionation. However, NO emissions from soils are usually small, posing major challenges to conversion efficiency and background contamination. Here we present a novel method in which NO is oxidized to NO2- by chromium trioxide (CrO3) prior to conversion to NO2- and NO3- in an alkaline hydrogen peroxide (H2O2) solution. Immediately following trapping, manganese dioxide (MnO2) and 5M HCl are added to remove excess H2O2, and to adjust the pH to around 6.0-7.0, respectively. The resulting solution can be stored until analysis and is none-toxic, allowing to use a modified denitrifier method (Zhu et al., submitted), where NO2- and NO3- are reduced quantitatively to nitrous oxide (N2O). Optimum NO conversion rates of > 90% even at extremely low initial NO concentration were obtained with 4% H2O2, 0.5 M NaOH, and 0.5 L min-1 gas flow rate. In a laboratory test, using NO gas with different 15N signals produced from unlabelled and labelled NO2-, we found an overall precision of 0.4‰ for unlabelled and 49.7‰ for NO enriched with 1.0 atom% 15N, respectively. This indicates that this method can be used for both natural abundance studies of NO, as well as in labelling studies tracing NO sources. Zhu J, Yu L, Bakken LR, Mørkved PT, Mulder J, Dörsch P. Controlled induction of denitrification in Pseudomonas aureofaciens: a modified denitrifier method for 15N and 18O analysis in NO3- from natural water samples by IRMS. Submitted.

  6. Dynamic of N fertilizers: urea (15 N) and aqua ammonia (15 N) incorporated to the sugar cane soil. Final report

    The dynamic of N fertilizers, urea and aqua ammonia, in the soil of sugar cane crops are studied with an emphasis on the horizontal and vertical moving. The nitrogen routing from urea and aqua ammonia sources, by isotopic technique with 15 N in relation to the leaching, volatilization and extraction by the cultivation and residue of N immobilized manure in the soil with sugar cane plantation is also analysed. (C.G.C.)

  7. Simple, efficient protocol for enzymatic synthesis of uniformly 13C, 15N-labeled DNA for heteronuclear NMR studies.

    Masse, J.E.; Bortmann, P; Dieckmann, T.; Feigon, J

    1998-01-01

    The use of uniformly 13C,15N-labeled RNA has greatly facilitated structural studies of RNA oligonucleotides by NMR. Application of similar methodologies for the study of DNA has been limited, primarily due to the lack of adequate methods for sample preparation. Methods for both chemical and enzymatic synthesis of DNA oligonucleotides uniformly labeled with 13C and/or 15N have been published, but have not yet been widely used. We have developed a modified procedure for preparing uniformly 13C,...

  8. /sup 15/N/sub 2/ incorporation and acetylene reduction by azospirillum isolated from rice roots and soils

    Nayak, D.N.; Charyulu, P.B.B.; Rajaramamohan Rao, V. (Central Rice Research Inst., Cuttack (India). Dept. of Soil Microbiology)

    1981-01-01

    Nitrogen fixation by strains of Azospirillum isolated from several rice soils and rice cultivars was investigated by /sup 15/N/sub 2/ incorporation and C/sub 2/H/sub 2/ reduction. C/sub 2/H/sub 2/ reducing ability markedly varied among the strains obtained from soils differing widely in their physico-chemical properties. Large variations in /sup 15/N/sub 2/ incorporation by Azospirillum isolated from the roots of several rice cultivars were also noticed. The present study reveals that rice cultivars harbour Azospirillum with differential N/sub 2/-fixing ability and that plant genotype is of importance for optimal associations.

  9. Recent advances in the application of 13C and 15N NMR spectroscopy to soil organic matter studies

    Nuclear magnetic resonance (NMR) spectroscopy has been applied to many studies in soil science, geochemistry, and environmental science. In recent years, the study of soil organic matter (SOM) using NMR techniques has progressed rapidly. NMR spectroscopy has been used to study chemical changes of SOM during decomposition, and also of soil extract fractions such as humic acid and fulvic acid. NMR spectroscopy of soils has improved rapidly in recent years with the introduction of pre-treatment and particle-size fractionation. In addition to routine liquid- and solid-state 13C NMR applications, 15N NMR spectra of natural abundant samples have been reported, but 15N-enriched material is more convenient to use due to the low natural abundance of 15N. Some newly developed NMR techniques have also been utilised, such as 2-dimensional NMR spectroscopy and improved 1H NMR techniques. These are reviewed and commented on in this paper. Copyright (2000) CSIRO Publishing

  10. Isotope 15N for agronomic research: an overview

    Fertilizer N recovery determined by isotope labelling technique using 15N enriched fertilizer was compared with apparent recovery of N obtained by the difference method and the extent of error associated with it was compared in six vegetable crops. In the difference method, fertilizer N recovery was overestimated and the error ranged from 3 per cent in tomato to 94 per cent in chilli, whereas uptake of soil N by the difference method was underestimated and the error ranged from 2 per cent in tomato to 64 per cent in chilli. One of the main reasons for the error was the degree of response to N due to increase in dry matter yield

  11. Orientation-dependent backbone-only residue pair scoring functions for fixed backbone protein design

    Bordner Andrew J

    2010-04-01

    Full Text Available Abstract Background Empirical scoring functions have proven useful in protein structure modeling. Most such scoring functions depend on protein side chain conformations. However, backbone-only scoring functions do not require computationally intensive structure optimization and so are well suited to protein design, which requires fast score evaluation. Furthermore, scoring functions that account for the distinctive relative position and orientation preferences of residue pairs are expected to be more accurate than those that depend only on the separation distance. Results Residue pair scoring functions for fixed backbone protein design were derived using only backbone geometry. Unlike previous studies that used spherical harmonics to fit 2D angular distributions, Gaussian Mixture Models were used to fit the full 3D (position only and 6D (position and orientation distributions of residue pairs. The performance of the 1D (residue separation only, 3D, and 6D scoring functions were compared by their ability to identify correct threading solutions for a non-redundant benchmark set of protein backbone structures. The threading accuracy was found to steadily increase with increasing dimension, with the 6D scoring function achieving the highest accuracy. Furthermore, the 3D and 6D scoring functions were shown to outperform side chain-dependent empirical potentials from three other studies. Next, two computational methods that take advantage of the speed and pairwise form of these new backbone-only scoring functions were investigated. The first is a procedure that exploits available sequence data by averaging scores over threading solutions for homologs. This was evaluated by applying it to the challenging problem of identifying interacting transmembrane alpha-helices and found to further improve prediction accuracy. The second is a protein design method for determining the optimal sequence for a backbone structure by applying Belief Propagation

  12. Theoretical study of the effective chemical shielding anisotropy (CSA) in peptide backbone, rating the impact of CSAs on the cross-correlated relaxations in L-alanyl-L-alanine

    Benda, Ladislav; Bouř, Petr; Müller, N.; Sychrovský, Vladimír

    2009-01-01

    Roč. 113, č. 15 (2009), s. 5273-5281. ISSN 1520-6106 R&D Projects: GA AV ČR IAA400550701; GA AV ČR IAA400550702; GA MŠk MEB060705 Institutional research plan: CEZ:AV0Z40550506 Keywords : chemical shielding anisotropy * CSA * L-alanyl-L-alanine Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.471, year: 2009

  13. An electron-scattering study of 15N

    An electron scattering experiment on 15N was performed in order to test the results of two different shell-model approaches, both performed in a full (0+2)ℎω space, one employing a phenomenologic interaction which is valid throughout the 1p shell, the other an interaction whose parameters were adjusted to fit the excitation energies of a number of states. The experiment was carried out at the high-energy electron-scattering facility of NIKHEF-k. A room temperature gas target was employed. Data were taken at forward angles in the range q=0.35 - 3.17 fm-1. Results are presented for negative-parity states up to an excitation energy of 13 MeV. The differences in groundstate charge density between 15N and the neighbouring nuclei 16O and 14N are compared with results of shell-model calculations. In ch. 5 the transition charge-densities to the excited negative-parity states are presented and compared with shell model calculations. 52 refs.; 18 figs.; 5 tabs

  14. Alterations in chemical shifts and exchange broadening upon peptide boronic acid inhibitor binding to α-lytic protease

    α-Lytic protease, a bacterial serine protease of 198 aminoacids (19800 Da), has been used as a model system for studies of catalytic mechanism, structure-function relationships, and more recently for studies of pro region-assisted protein folding. We have assigned the backbones of the enzyme alone, and of its complex with the tetrahedral transition state mimic N-tert-butyloxycarbonyl-Ala-Pro-boroVal, using double- and triple-resonance 3D NMR spectroscopy on uniformly15N- and 13C/15N-labeled protein.Changes in backbone chemical shifts between the uncomplexed and inhibited form of the protein are correlated with distance from the inhibitor, the displacement of backbone nitrogens, and change in hydrogen bond strength upon inhibitor binding (derived from previously solved crystal structures).A comparison of the solution secondary structure of the uninhibited enzyme with that of the X-ray structure reveals no significant differences.Significant line broadening, indicating intermediate chemical exchange, was observed in many of the active site amides (including three broadened to invisibility), and in a majority of cases the broadening was reversed upon addition of the inhibitor. Implications and possible mechanisms of this line broadening are discussed

  15. Net neutrality at internet backbone provider level

    Baglioni, Laura; Calabrese, Armando; Ghiron, Nathan Levialdi

    2013-01-01

    This paper analysis the Internet interconnection market and combine the main technical (i.e. service quality) and economic aspects (i.e. profits and utility) characterizing relations between market players (end users, EUs; Internet Service Providers, ISPs; Internet Backbone Providers, IBPs) in order to determine possible economic outcomes in the strategic interaction between them. The proposed model enables a comparison to be made between expected values of social welfare (i.e. EU utility and...

  16. Hash: a program to accurately predict protein H{sup {alpha}} shifts from neighboring backbone shifts

    Zeng Jianyang, E-mail: zengjy@gmail.com [Tsinghua University, Institute for Interdisciplinary Information Sciences (China); Zhou Pei [Duke University Medical Center, Department of Biochemistry (United States); Donald, Bruce Randall [Duke University, Department of Computer Science (United States)

    2013-01-15

    Chemical shifts provide not only peak identities for analyzing nuclear magnetic resonance (NMR) data, but also an important source of conformational information for studying protein structures. Current structural studies requiring H{sup {alpha}} chemical shifts suffer from the following limitations. (1) For large proteins, the H{sup {alpha}} chemical shifts can be difficult to assign using conventional NMR triple-resonance experiments, mainly due to the fast transverse relaxation rate of C{sup {alpha}} that restricts the signal sensitivity. (2) Previous chemical shift prediction approaches either require homologous models with high sequence similarity or rely heavily on accurate backbone and side-chain structural coordinates. When neither sequence homologues nor structural coordinates are available, we must resort to other information to predict H{sup {alpha}} chemical shifts. Predicting accurate H{sup {alpha}} chemical shifts using other obtainable information, such as the chemical shifts of nearby backbone atoms (i.e., adjacent atoms in the sequence), can remedy the above dilemmas, and hence advance NMR-based structural studies of proteins. By specifically exploiting the dependencies on chemical shifts of nearby backbone atoms, we propose a novel machine learning algorithm, called Hash, to predict H{sup {alpha}} chemical shifts. Hash combines a new fragment-based chemical shift search approach with a non-parametric regression model, called the generalized additive model, to effectively solve the prediction problem. We demonstrate that the chemical shifts of nearby backbone atoms provide a reliable source of information for predicting accurate H{sup {alpha}} chemical shifts. Our testing results on different possible combinations of input data indicate that Hash has a wide rage of potential NMR applications in structural and biological studies of proteins.

  17. Backbone Dynamics of Triple-helical Collagen-like Structure

    Lazarev, Yu.A.; Lazareva, A.V.; Komarov, V.M.

    1999-01-01

    Some details of the backbone dynamics in the collagen-like triple helix is discussed and the role of backbone dynamics in functioning collagen proteins is illustrated. On a series of oligotripeptides synthetic analogs of collagen formation of high-frequency vibrational backbone dynamics and low-frequency nonlinear backbone dynamics upon stepwise elongation of peptide chain have been described using infrared spectroscopy and hydrogen-exchange method. In the fully completed triple helix the lev...

  18. Natural abundance of /sup 15/N in soil organic matter with special reference to paddy soils in Japan. Biogeochemical implications on the nitrogen cycle

    Wada, Eitaro; Imaizumi, Reiko (Mitsubishi Chemical Industries Ltd., Tokyo (Japan)); Takai, Yasuo

    1984-01-01

    In order to explain the general principle which controls the /sup 15/N content of soil organic nitrogen, experimental rice fields which were fertilized for long term were investigated. The /sup 15/N abundance values of rice plants vary according to the kinds of fertilizer, e.g., chemical fertilizer and green manure. The significant difference of /sup 15/N abundance was recognized between rice plants and fertilizers. Nitrification and denitrification seemed to be responsible for the difference. But these have minor effect on the variation of /sup 15/N abundance of soil because rice plants assimilate all available nitrogen and are removed from paddy fields by harvest. Consequently, the effects of nitrification-denitrification and ammonia volatilization are observed only in biological process such as the growth of rice plants and hydrophytes. A long term addition of fertilizers clearly increased the amount of soil organic nitrogen in paddy fields. Based on isotope mass balance, nitrogen isotope fractionation factor of 0.9942 was estimated in the process of epidiagenesis which indicates the selective decomposition of heavy isotopic species. An addition of ammonium sulfate with low /sup 15/N abundance decreased the /sup 15/N content of soil nitrogen in the paddy fields with the depletion of soil organic nitrogen. OrgC/clay ratio was demonstrated as an important factor which controls the /sup 15/N abundance value in paddy soil. The relation between the /sup 15/N abundance value in soil organic nitrogen and OrgC/clay ratio was able to be presented by hyperbola for the paddy soild so far examined. The /sup 15/N abundance of source and plant nitrogen two isotopic fractionation associated with the epidiagenesis of soil organic matter and the adsorption of ammonia by clay minerals are the three major factors determining the /sup 15/N abundance of soil organic nitrogen.

  19. Application of δ13C and δ15N isotopic signatures of organic matter fractions sequentially separated from adjacent arable and forest soils to identify carbon stabilization mechanisms

    Kayler, Z.E.; Kaiser, M; Gessler, A.; Ellerbrock, R. H.; M. Sommer

    2011-01-01

    Identifying the chemical mechanisms behind soil carbon bound in organo-mineral complexes is necessary to determine the degree to which soil organic carbon is stabilized belowground. Analysis of δ13C and δ15N isotopic signatures of stabilized OM fractions along with soil mineral characteristics may yield important information about OM-mineral associations and their processing history. We anlayzed the δ13C and δ15N isotopic signatures from two organic matter (OM) fractio...

  20. Effect of fed-batch on synthesis of 15N-L-tryptophan from precursor fermentation

    Using Candida utilis AS60 as 15N-L-tryptophan producing strain, the influence by different feeding modes of glucose, 15N-(NH4)2SO4 and 15N-anthranilic acid was studied. The results of these experiments show that the yield of 15N-L-tryptophan was 3.073 g/L by addition of 50 g/L of glucose, 2.1 g/L of 15N-(NH4)2SO4 and 1.5 g/L of 15N-anthranilic acid after 36 h of fermentation. (authors)

  1. A synthetic HIV-1 subtype C backbone generates comparable PR and RT resistance profiles to a subtype B backbone in a recombinant virus assay.

    David Nauwelaers

    Full Text Available In order to determine phenotypic protease and reverse transcriptase inhibitor-associated resistance in HIV subtype C virus, we have synthetically constructed an HIV-1 subtype C (HIV-1-C viral backbone for use in a recombinant virus assay. The in silico designed viral genome was divided into 4 fragments, which were chemically synthesized and joined together by conventional subcloning. Subsequently, gag-protease-reverse-transcriptase (GPRT fragments from 8 HIV-1 subtype C-infected patient samples were RT-PCR-amplified and cloned into the HIV-1-C backbone (deleted for GPRT using In-Fusion reagents. Recombinant viruses (1 to 5 per patient sample were produced in MT4-eGFP cells where cyto-pathogenic effect (CPE, p24 and Viral Load (VL were monitored. The resulting HIV-1-C recombinant virus stocks (RVS were added to MT4-eGFP cells in the presence of serial dilutions of antiretroviral drugs (PI, NNRTI, NRTI to determine the fold-change in IC50 compared to the IC50 of wild-type HIV-1 virus. Additionally, viral RNA was extracted from the HIV-1-C RVS and the amplified GPRT products were used to generate recombinant virus in a subtype B backbone. Phenotypic resistance profiles in a subtype B and subtype C backbone were compared. The following observations were made: i functional, infectious HIV-1 subtype C viruses were generated, confirmed by VL and p24 measurements; ii their rate of infection was slower than viruses generated in the subtype B backbone; iii they did not produce clear CPE in MT4 cells; and iv drug resistance profiles generated in both backbones were very similar, including re-sensitizing effects like M184V on AZT.

  2. Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters

    Zgarbová, M.; Luque, F. J.; Šponer, Jiří; Cheatham III, Thomas E.; Otyepka, M.; Jurečka, P.

    2013-01-01

    Roč. 9, č. 5 (2013), s. 2339-2354. ISSN 1549-9618 Grant ostatní: GA ČR(CZ) GAP208/10/1742 Institutional support: RVO:68081707 Keywords : MOLECULAR- DYNAMICS SIMULATIONS * PHOSPHORUS CHEMICAL-SHIFTS * SUGAR-PHOSPHATE BACKBONE Subject RIV: BO - Biophysics Impact factor: 5.310, year: 2013

  3. Investigation of the metabolism of colostomized laying hens with 15N-labelled wheat. 6

    Three colostomized laving hens received 40 g 15N-labelled wheat with 20.13 atom-% 15N excess (15N'), 19.18 atom-% 15N'-lysine, 18.17 atom-% 15N'-histidine and 20.43 atom-% 15N'-arginine per day over a period of four days. After having received the same non-labelled feed ration on the following four days, the hens were slaughtered. The incorporation and distribution of 15N' in the total nitrogen and the nitrogen of the basic amino acids was determined in liver, kidneys, muscles, bones and the remaining carcass (excluding blood, digestive tract and genital organs). The quota of nitrogen of natural isotope frequency (14N) of the total 14N of the hens' carcasses was 47% in the muscles, 14% in the bones and 20% in the feathers; the relative 15N' values were 37%, 8% and 1%, resp. The atom-% 15N' in the kidneys was twice as much as in the liver four days after the last 15N' application. The average percentage of the nitrogen in the three basic amino acids of the total nitrogen in the tissues and organs (excluding feathers) is 25% concerning both 14N and 15N'. The 15N' balance revealed that in hen 1 100%, in hen 2 102% and in hen 3 101% of the consumed wheat 15N' were found. (author)

  4. SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network

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

    2010-09-15

    NMR chemical shifts provide important local structural information for proteins and are key in recently described protein structure generation protocols. We describe a new chemical shift prediction program, SPARTA+, which is based on artificial neural networking. The neural network is trained on a large carefully pruned database, containing 580 proteins for which high-resolution X-ray structures and nearly complete backbone and {sup 13}C{sup {beta}} chemical shifts are available. The neural network is trained to establish quantitative relations between chemical shifts and protein structures, including backbone and side-chain conformation, H-bonding, electric fields and ring-current effects. The trained neural network yields rapid chemical shift prediction for backbone and {sup 13}C{sup {beta}} atoms, with standard deviations of 2.45, 1.09, 0.94, 1.14, 0.25 and 0.49 ppm for {delta}{sup 15}N, {delta}{sup 13}C', {delta}{sup 13}C{sup {alpha}}, {delta}{sup 13}C{sup {beta}}, {delta}{sup 1}H{sup {alpha}} and {delta}{sup 1}H{sup N}, respectively, between the SPARTA+ predicted and experimental shifts for a set of eleven validation proteins. These results represent a modest but consistent improvement (2-10%) over the best programs available to date, and appear to be approaching the limit at which empirical approaches can predict chemical shifts.

  5. SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network

    NMR chemical shifts provide important local structural information for proteins and are key in recently described protein structure generation protocols. We describe a new chemical shift prediction program, SPARTA+, which is based on artificial neural networking. The neural network is trained on a large carefully pruned database, containing 580 proteins for which high-resolution X-ray structures and nearly complete backbone and 13Cβ chemical shifts are available. The neural network is trained to establish quantitative relations between chemical shifts and protein structures, including backbone and side-chain conformation, H-bonding, electric fields and ring-current effects. The trained neural network yields rapid chemical shift prediction for backbone and 13Cβ atoms, with standard deviations of 2.45, 1.09, 0.94, 1.14, 0.25 and 0.49 ppm for δ15N, δ13C', δ13Cα, δ13Cβ, δ1Hα and δ1HN, respectively, between the SPARTA+ predicted and experimental shifts for a set of eleven validation proteins. These results represent a modest but consistent improvement (2-10%) over the best programs available to date, and appear to be approaching the limit at which empirical approaches can predict chemical shifts.

  6. Porous solid backbone impregnation for electrochemical energy conversion systems

    Boulfrad, Samir

    2013-09-19

    An apparatus and method for impregnating a porous solid backbone. The apparatus may include a platform for holding a porous solid backbone, an ink jet nozzle configured to dispense a liquid solution onto the porous solid backbone, a positioning mechanism configured to position the ink jet nozzle proximate to a plurality of locations of the porous solid backbone, and a control unit configured to control the positioning mechanism to position the ink jet nozzle proximate to the plurality of locations and cause the ink jet nozzle to dispense the liquid solution onto the porous solid backbone.

  7. Backbone Guided Local Search for the Weighted Maximum Satisfiability Problem

    Jiang, He; Xuan, Jifeng

    2009-01-01

    In this chapter, analytical results on the backbone in weighted MAX-SAT were presented in this paper. We showed that it is intractable to retrieve the backbone in weighted MAX-SAT with any performance guarantee under the assumption that P NP . And a backbone guided local search algorithm was proposed for weighted MAX-SAT. Results of this paper imply a new way to incorporate the backbone in heuristics. The approximate backbone used to guide the flipping of literals in those local search based...

  8. Convenient and scalable synthesis of fmoc-protected Peptide nucleic Acid backbone.

    Feagin, Trevor A; Shah, Nirmal I; Heemstra, Jennifer M

    2012-01-01

    The peptide nucleic acid backbone Fmoc-AEG-OBn has been synthesized via a scalable and cost-effective route. Ethylenediamine is mono-Boc protected, then alkylated with benzyl bromoacetate. The Boc group is removed and replaced with an Fmoc group. The synthesis was performed starting with 50 g of Boc anhydride to give 31 g of product in 32% overall yield. The Fmoc-protected PNA backbone is a key intermediate in the synthesis of nucleobase-modified PNA monomers. Thus, improved access to this molecule is anticipated to facilitate future investigations into the chemical properties and applications of nucleobase-modified PNA. PMID:22848796

  9. Understanding VoIP from Backbone Measurements

    Birke, Robert Rene' Maria; Petracca, Michele; Mellia, Marco

    2007-01-01

    VoIP has widely been addressed as the technology that will change the Telecommunication model opening the path for convergence. Still today this revolution is far from being complete, since the majority of telephone calls are originated by circuit-oriented networks. In this paper for the first time to the best of our knowledge, we present a large dataset of measurements collected from the FastWeb backbone, which is one of the first worldwide Telecom operator to offer VoIP and high-speed data ...

  10. Peptoid-Peptide hybrid backbone architectures

    Olsen, Christian Adam

    2010-01-01

    Peptidomimetic oligomers and foldamers have received considerable attention for over a decade, with beta-peptides and the so-called peptoids (N-alkylglycine oligomers) representing prominent examples of such architectures. Lately, hybrid or mixed backbones consisting of both alpha- and beta......-amino acids (alpha/beta-peptides) have been investigated in some detail as well. The present Minireview is a survey of the literature concerning hybrid structures of alpha-amino acids and peptoids, including beta-peptoids (N-alkyl-beta-alanine oligomers), and is intended to give an overview of this area...

  11. Determination of 15N nitrates in water samples using mass spectrometry

    The nitrogen element (Z = 7) has two stable isotopes, whose relative quantities are 99.64% for 14N and 0.36% for 15N. Nitrogen is part of many processes and reactions that are important to life and that affect the quality of the water. Within the nitrogen cycle there are kinetic and thermodynamic fractionation processes, which are potentially important for tracing its sources and demands. Water contamination due to nitrates is a serious problem that is affecting large parts of the biosphere. Surface water contamination can be remedied by prevention and control measures, but the problem becomes acute when the contamination penetrates to groundwater water. Contaminated groundwater can remain in the aquifers for centuries, even milleniums, and decontamination is very difficult, if not impossible. Isotopic techniques can help to evaluate how vulnerable the groundwater is to contamination from the surface when its displacement speed and extra load area are determined. Then the sources of surface contamination (natural, industrial, agricultural, domestic) can be identified. Isotopic techniques can also describe an incipient contamination, and they can provide an early alert when chemical or biological indicators do not reveal any signs for concern. The isotopic fractionation of several nitrogen compounds provide the basis for using 15N as a hydrological isotope tool. There are three main sources of nitrogen contamination in water, these are: organic nitrogen in the soil, nitrogenized fertilizers, domestic, industrial and animal wastes. The following technical procedure describes the method for determining the isotopic ration 15N/14N in nitrates in water. The nitrate is separated from the water using ion exchange columns through a resin, which is eluded with HCI and with the addition of silver oxide becomes silver nitrate. This solution is freeze-dried and submitted to combustion at 850 in a sealed quartz tube, using copper/copper oxide for the nitrogen reduction and

  12. Use of Bio-Organic Fertilizers to Develop N Uptake Using 15N Technique

    Experimental work either in field scale or in green house conditions were conducted using 15N technique to evaluate the role of different bio fertilizers and different plant residues as organic amendments on enhancement of plant N nutrition. Nitrogen fixation by a symbiotic bacteria has been observed in greenhouse and field experiments under dry land cropping systems. Biological N2 fixation associated with crop residues (legumes or cereals) was investigated in pot experiments with wheat and chickpea cultivars. In these experiments, labelled wheat and rice straw were used as organic N sources in comparison with either 15N-labelled ammonium sulfate or ammonium nitrate as chemical nitrogen fertilizers. Rhizobium inoculation extended to be used with wheat gave the best results of N uptake and N2 fixation when combined with Azospirillum brasilense as heterotrophic diazotrophs. The nitrogen uptake by wheat plants was significantly increased by application of soybean residues and inoculation with Azospirillum brasilense. From the field trial we can conclude that soybean residue as enriched N material, and Azospirillum brasilense inoculation enhanced N yields of wheat cultivars grown in poor fertile sandy soil

  13. Impact of Backbone Fluorination on π-Conjugated Polymers in Organic Photovoltaic Devices: A Review

    Nicolas Leclerc

    2016-01-01

    Full Text Available Solution-processed bulk heterojunction solar cells have experienced a remarkable acceleration in performances in the last two decades, reaching power conversion efficiencies above 10%. This impressive progress is the outcome of a simultaneous development of more advanced device architectures and of optimized semiconducting polymers. Several chemical approaches have been developed to fine-tune the optoelectronics and structural polymer parameters required to reach high efficiencies. Fluorination of the conjugated polymer backbone has appeared recently to be an especially promising approach for the development of efficient semiconducting polymers. As a matter of fact, most currently best-performing semiconducting polymers are using fluorine atoms in their conjugated backbone. In this review, we attempt to give an up-to-date overview of the latest results achieved on fluorinated polymers for solar cells and to highlight general polymer properties’ evolution trends related to the fluorination of their conjugated backbone.

  14. Metabolic studies in colostomized laying hens using 15N-labelled wheat. 4

    3 colostomized laying hybrids received over 4 days a dosage of 672 mg 15N excess (15N'), 20.3 mg lysine 15N', 23.0 mg histidine 15N' and 66.7 mg arginine 15N' with a ration customary in production. After feeding the same unlabelled ration for another 4 days the hens were killed and the N content of the blood as well as of its fractions (cells, plasma, free amino acids of the plasma) was determined. The 15N' was determined in the total blood, the corpuscles, the plasma, the nonprotein-N (NPN) fraction as well as in the amino acids lysine, histidine and arginine. The average amount of the blood cell N in the total blood N was 58.5% and that of the plasma 40.3%; the corresponding 15N' values amounted to 66.1% and 33.9%, respectively. The sum of the 15N' of the basic amino acids of the blood cells, on an average, amounted to 39.7% of the total cell 15N'; the corresponding average value for the total 15N' in lysine, histidine and arginine of the blood plasma 15N' was 23.6.% and the quota of the three free amino acids of the total NP15N' of the plasma was 6.2%. (author)

  15. Utilization of natural variations in the isotopic abundance of 15N to trace the source of aquifer pollution by nitrates

    The validity of using the natural isotope nitrogen-15 to trace the source of nitrates contained in aquifers is discussed with reference to experimental devices (lysimeters and experimental plots) and for examples chosen from the Paris area. There are a number of sources of nitrates: (1) industrially synthesized nitrates (fertilizers); (2) nitrates produced by oxidation of organic matter associated with human, agricultural or urban activities; (3) nitrates synthesized in the soil by the decay of organic matter. In the examples studied these sources differ in their 15N content: (1) fertilizers have a delta15N close to zero (atmospheric nitrogen); (2) the nitrates originating from organic pollution have high delta15N (above 10-12 per mille) and this 15N enrichment is associated with the volatilization of ammonia during the ammonia stage of mineralization; (3) the isotopic characterization of the nitrates produced by organic matter in the soil is less evident. Citing several examples, the author demonstrates that these three sources are diffentiated isotopically. Consideration of the parameters nitrate concentration/isotopic composition reveals simple mixture curves. In the most complicated cases - where there is association with other isotopic (3H) or chemical parameters - it is possible qualitatively to trace the sources of nitrogen pollution

  16. FAO/IAEA - interregional training course on the use of 15N in soil science and plant nutrition

    This training manual provides an introduction for the basic methodology and principles of application of the stable isotope 15N. After preliminary remarks on stable isotope terminology fundamentals, experimental problems and methods of quantitative nitrogen determination in soil and plant studies are reported in the main part of the manual. An appendix with a compilation of different parameters such as natural abundance of stable isotopes, selected atomic weights and multiples of them conversion factors of chemical compounds, and much more concludes the manual

  17. Fate of 15N-urea and 15N-ammonium sulphate applied in different periods to cica-8 rice culture in greenhouse conditions

    The fate of nitrogen fertilizers in rice cultivars (Cica-8) is studied. Urea (1.973% at of 15N) and ammonium sulfate (1.826% at of 15N) are used. The fertilizers are applied in four levels (0,100,200 and 300 Kg N/ha) in shadow coditions and after 30 days of germination. (M.A.C.)

  18. Mechanism of Solid-State Thermolysis of Ammonia Boraine: 15N NMR Study Using Fast Magic-Angle Spinning and Dynamic Nuclear Polarization

    Kobayashi, Takeshi [Ames Laboratory; Gupta, Shalabh [Ames Laboratory; Caporini, Marc A [Bruker BioSpin Corporation; Pecharsky, Vitalij K [Ames Laboratory; Pruski, Marek [Ames Laboratory

    2014-08-28

    The solid-state thermolysis of ammonia borane (NH3BH3, AB) was explored using state-of-the-art 15N solid-state NMR spectroscopy, including 2D indirectly detected 1H{15N} heteronuclear correlation and dynamic nuclear polarization (DNP)-enhanced 15N{1H} cross-polarization experiments as well as 11B NMR. The complementary use of 15N and 11B NMR experiments, supported by density functional theory calculations of the chemical shift tensors, provided insights into the dehydrogenation mechanism of AB—insights that have not been available by 11B NMR alone. Specifically, highly branched polyaminoborane derivatives were shown to form from AB via oligomerization in the “head-to-tail” manner, which then transform directly into hexagonal boron nitride analog through the dehydrocyclization reaction, bypassing the formation of polyiminoborane.

  19. Precision and sensitivity of the measurement of 15N enrichment in D-alanine from bacterial cell walls using positive/negative ion mass spectrometry

    Tunlid, A.; Odham, G.; Findlay, R. H.; White, D. C.

    1985-01-01

    Sensitive detection of cellular components from specific groups of microbes can be utilized as 'signatures' in the examination of microbial consortia from soils, sediments or biofilms. Utilizing capillary gas chromatography/mass spectrometry and stereospecific derivatizing agents, D-alanine, a component localized in the prokaryotic (bacterial) cell wall, can be detected reproducibly. Enrichments of D-[15N]alanine determined in E. coli grown with [15N]ammonia can be determined with precision at 1.0 atom%. Chemical ionization with methane gas and the detection of negative ions (M - HF)- and (M - F or M + H - HF)- formed from the heptafluorobutyryl D-2 butanol ester of D-alanine allowed as little as 8 pg (90 fmol) to be detected reproducibly. This method can be utilized to define the metabolic activity in terms of 15N incorporation at the level of 10(3)-10(4) cells, as a function of the 15N-14N ratio.

  20. Utilization of 15N-labelled urea in laying hens. 4

    In order to study the utilization of urea in poultry, 3 colostomized laying hybrids were orally supplied with a traditional ration supplemented with 1% 15N'-labelled urea with a 15N excess (15N') of 96.06 atom-% over a period of 6 days. After another 2 days on which the hens received the same ration with unlabelled urea, they were killed. The atom-% 15N' of the blood on an average of the 3 hens was 0.64, of the plasma 1.40 and of the corpuscles 0.47. The TCA-soluble fraction of the blood had an average 15N' of 1.14 atom-%; the 15N amount was 9.7% of the total amount of 15N in the blood. The amount of 15N' in the urea in the blood was 6.8 atom-%. This shows that the absorbed urea is decomposed very slowly. The quota of 15N' in the basic amino acids from the total 15N' of the blood plasma was only 0.3% and that of the corpuscles 2.2%. The average 15N' of the mature follicles was 2.39 atom-% whereas the smallest and the remaining ovary contain 1.12 atom-%. The labelling level of lysine in mature egg cells was, in contrast to this, only 0.08 atom-% 15N' and in infantile follicles 0.04 atom-% 15N'. 1% of the 15N' quota was in the follicles and the remaining ovary. Of the basic amino acids, histidine is most strongly labelled. The lower incorporation of the 15N' from urea into the basic amino acids shows that the nitrogen of this compound can be used for the synthesis of the essential amino acids to a low degree only. (author)

  1. Backbone and side-chain 1H, 13C and 15N assignments of the ubiquitin-associated domain of human X-linked inhibitor of apoptosis protein

    Hui, Sin-Kam; Tse, Man-Kit; Yang, Yinhua; Wong, Benjamin Chun-Yu; Sze, Kong-Hung

    2010-01-01

    X-linked inhibitor of apoptosis protein (XIAP), a leading member of the family of inhibitor of apoptosis (IAP) proteins, is considered as the most potent and versatile inhibitor of caspases and apoptosis. It has been reported that XIAP is frequently overexpressed in cancer and its expression level is implicated in contributing to tumorigenesis, disease progression, chemoresistance and poor patient-survival. Therefore, XIAP is one of the leading targets in drug development for cancer therapy. ...

  2. The influence of DNA binding on the backbone dynamics of the yeast cell-cycle protein Mbp1

    Mbp1 is a transcription factor involved in the regulation of the cell cycle in yeast. The N-terminus of this protein contains a DNA binding domain that includes a winged helix-turn-helix motif. The C-terminal 24 residues of this domain (the 'tail') are disordered in the crystal state, but are important for DNA binding. We have measured 15N NMR relaxation rates at 11.75 and 14.1 T to determine the dynamics of the free protein and in its complex with a specific DNA duplex. The dynamics data were quantitatively analysed using both spectral density mapping and the Lipari-Szabo formalism including the effects of chemical exchange and rotational anisotropy. A detailed analysis has been made of the effect of anisotropy, exchange and experimental precision on the recovered motional parameters. The backbone NH relaxation is affected by motions on a variety of time scales from millisecond to tens of picoseconds. The relaxation data show a structured core of 100 residues corresponding to that observed in the crystal state. Within the core of the protein, two regions on either side of the putative recognition helix (helix B) show slow (ca. 0.2 ms) conformational exchange dynamics that are quenched upon DNA binding. The C-terminal 24 residues are generally more dynamic than in the core. However, in the free protein, a stretch of ∼8 residues in the middle of the tail show relaxation behaviour similar to that in the core, indicating a structured region. NOEs between Ala 114 in this structured part of the tail and residues in the N-terminal beta strand of the core of the protein demonstrate that the tail folds back onto the core of the protein. In the complex with DNA, the structured part of the tail extends by ca. 3 residues. These data provide a framework for understanding the biochemical data on the mechanism and specificity of DNA binding

  3. The synthesis of barbituric acid and some of its derivatives isotopically labelled with 15N

    Full text: Barbituric acid is the parent compound of a large class of barbiturates that have central nervous system depressant properties, although barbituric acid itself is not pharmacologically active. In recent years, barbituric acid derivatives have been studied as antitumor, anticancer and anti-osteoporosis agents. The aim of this paper is to present the synthesis of barbituric acid-15N, 5,5-diethylbarbituric acid-15N (Veronal-15N) and 5-ethyl-5-phenylbarbituric acid- 15N (Phenobarbitone-15N) . As isotopically labelled material we used urea-15N2, 99 at.% 15N produced at National Institute for Research and Development of Isotopic and Molecular Technologies, Cluj-Napoca, Romania. All compounds were fully characterized by Mass Spectrometry analyses, by FT-IR Spectroscopy and RX Diffraction, and the isotopic label was determined by MS on the molecular compounds. (author)

  4. Pion elastic and inelastic scattering from 15N

    Data were obtained on the Clinton P. Anderson Los Alamos Meson Physics Facility Energetic Pion Channel and Spectrometer for elastic and inelastic pion scattering from ground state 15N nuclei. States observed here included those of 0.0, 5.27, 6.32, 7.16, 7.30, 7.57, 8.31, 8.57, 9.15, 9.76, 9.9, 10.7, 11.3, 11.9, 12.5, 12.9, 13.1, 14.1, 14.4, 14.6, 15.0, 16.5, 16.9, 17.2, 17.6, 18.3, 18.7, and 18.9 MeV excitation energies. Angular distributions were obtained for scattering at angles from 25 degree to 90 degree in 5 degree increments with an incident pion energy of 164 MeV. Optical model analyses of the elastic (0 MeV) angular distributions with equal point proton and neutron densities in both momentum and coordinate space formulations accurately predict the data, although the two formulations require different energy shifts to do so. This difference is thought to be a result of the more accurate nonlocal representation of the nuclear potential in the momentum space code. Additional spectra were obtained for scattering at constant momentum transfers of .94 and 1.57 fm-1 in order to generate constant momentum transfer excitation functions. Use of these excitation functions, σ(π+)/σ(π-) ratios, and shell model DWIA calculations allowed identification of several excited states having shell-model-like, single particle-hole, pure spin-flip excitations. Shell model and collective model DWIA calculations, as well as the q = .94 and 1.57 fm-1 excitation functions and the σ(π+)/σ(π-) ratios indicate that the other states are generally well represented by a shell model description with collective enhancements

  5. Studies with 15N-labelled lysine in colostomized laying hens. 5

    3 colostomized laying hens received, together with a commercial ration of 120 g, 0.2 % 15N-labelled L-lysine with an atom-% 15N excess (15N') of 48 %; subsequently the same ration was fed over a period od 4 days with 0.2 % unlabelled L-lysine. After the end of the experiment the hens were slaughtered. The atom-% 15N' was determined in total, in the lysine, histidine and arginine N of blood cells, plasma, NPN fraction of the blood, stomach, small intestine, cecum and rectum. 15N' in the blood cells was 0.11 atom-% in the blood plasma 0.17 atom-%, in the NPN fraction of the blood 0.09 atom-%, in the tissues of the gastrointestinal tract 0.11 atom-% and in its contents 0.12 atom-%. On the average the blood contained per hen 77.9 % lysine-15N', 16.4 % arginine-15N' and 5.7 % histidine-15N' of the basic amino acid-15N'. For the gastrointestinal tract 78.7 % lysine-15N', 19.0 % arginine-15N' and 2.3 % histidine-15N' of the 15N' of the basic amino acids were ascertained. In comparison to histidine the α-amino-N of lysine is incorporated to a considerably higher degree into arginine. For lysine and arginine the atom-% 15N' in the contents of the gastrointestinal tract is 4 days after the end of the supplementation of labelled lysine 8 to 10 times higher than in the feces of the last day of the experiment. This indicates a considerable secretion of the 2 amino acids in the gastrointestinal tract and their reabsorption to a large extent. (author)

  6. Improved 3D triple resonance experiments, HNN and HN(C)N, for HN and 15N sequential correlations in (13C, 15N) labeled proteins: Application to unfolded proteins

    Panchal, Sanjay C.; Bhavesh, Neel S.; Hosur, Ramakrishna V. [Tata Institute of Fundamental Research, Department of Chemical Sciences (India)

    2001-06-15

    Two triple resonance experiments, HNN and HN(C)N, are presented which correlate H{sup N} and {sup 15}N resonances sequentially along the polypeptide chain of a doubly ({sup 13}C, {sup 15}N) labeled protein. These incorporate several improvements over the previously published sequences for a similar purpose and have several novel features. The spectral characteristics enable direct identification of certain triplets of residues, which provide many starting points for the sequential assignment procedure. The experiments are sensitive and their utility has been demonstrated with a 22 kDa protein under unfolding conditions where most of the standard triple resonance experiments such as HNCA, CBCANH etc. have limited success because of poor amide, C{sup {alpha}} and C{sup {beta}} chemical shift dispersions.

  7. Improved 3D triple resonance experiments, HNN and HN(C)N, for HN and 15N sequential correlations in (13C, 15N) labeled proteins: Application to unfolded proteins

    Two triple resonance experiments, HNN and HN(C)N, are presented which correlate HN and 15N resonances sequentially along the polypeptide chain of a doubly (13C, 15N) labeled protein. These incorporate several improvements over the previously published sequences for a similar purpose and have several novel features. The spectral characteristics enable direct identification of certain triplets of residues, which provide many starting points for the sequential assignment procedure. The experiments are sensitive and their utility has been demonstrated with a 22 kDa protein under unfolding conditions where most of the standard triple resonance experiments such as HNCA, CBCANH etc. have limited success because of poor amide, Cα and Cβ chemical shift dispersions

  8. 15N tracer kinetic studies on the validity of various 15N tracer substances for determining whole-body protein parameters in very small preterm infants

    Reliable 15N tracer substances for tracer kinetic determination of whole-body protein parameters in very small preterm infants are still a matter of intensive research, especially after some doubts have been raised about the validity of [15N]glycine, a commonly used 15N tracer. Protein turnover, synthesis, breakdown, and further protein metabolism data were determined by a paired comparison in four preterm infants. Their post-conceptual age was 32.2 +/- 0.8 weeks, and their body weight was 1670 +/- 181 g. Tracer substances applied in this study were a [15N]amino acid mixture (Ia) and [15N]glycine (Ib). In a second group of three infants with a post conceptual age of 15N-labeled 32.0 +/- 1.0 weeks and a body weight of 1,907 +/- 137 g, yeast protein hydrolysate (II) was used as a tracer substance. A three-pool model was employed for the analysis of the data. This model takes into account renal and fecal 15N losses after a single 15N pulse. Protein turnovers were as follows: 11.9 +/- 3.1 g kg-1 d-1 (Ia), 16.2 +/- 2.5 g kg-1 d-1 (Ib), and 10.8 +/- 3.0 g kg-1 d-1 (II). We were able to demonstrate an overestimation of the protein turnover when Ib was used. There was an expected correspondence in the results obtained from Ia and II. The 15N-labeled yeast protein hydrolysate is a relatively cheap tracer that allows reliable determination of whole-body protein parameters in very small preterm infants

  9. Use of 15N Label in Organic Synthesis and Spectroscopy. Part I: Preparation of 15N-Labeled tert-Butylamine

    Talaty, Erach R.; Boese, Christopher A.; Adewale, Sanni M.; Ismail, Mohammed S.; Provenzano, Frank A.; Utz, Melissa J.

    2002-02-01

    The preparation of 15N-labeled tert-butylamine involves the conversion of the correspondingly labeled potassium cyanide into the 15N-labeled tert-butylformamide via the Ritter reaction in 85% yield, followed by hydrolysis with either aqueous sodium hydroxide or hydrochloric acid. The NMR spectra of the compounds provide a valuable opportunity for discussing several important topics in NMR spectroscopy, such as cis-trans isomerism due to restricted rotation and 15N coupling. Comparison of the IR spectra of the labeled and unlabeled compounds permits a forum for discussing the theory of vibrational frequencies.

  10. Studies with 15N-labelled lysine in colostomized hens. 3

    In a metabolism experiment with 15N-labelled lysine 3 colostomized laying hybrids received over 4 days 0.2% L-lysine with 48 at% 15N excess (15N') in addition to a ration conventionally produced and, subsequent to this, unlabelled lysine for four days. At the end of the experiment the hens were killed and the individual organs and tissues were prepared for 15N analysis. The incorporation of the lysine-15N' into the further amino acids of follicles, ovary and oviduct is described. The at% 15N' of the complete range of amino acids was analyzed in the individual follicles. Various levels of heavy nitrogen could be detected in all essential and non-essential amino acids. Of the total amount of 15N' detected in the follicles 64.0%, 65.0% and 61.2%, resp., could be detected in lysine and 25.2%, 25.4% and 28.7%, resp., in the other amino acids (hens 1 to 3). In the ovary on average 61.6% and in the oviduct 54.2% of the respective 15N' amount was detected in lysine. In the ovary 10.9% and in the oviduct 8.4% 15N' of the total 15N' of these samples were incorporated into the arginine molecules. (author)

  11. Alanine flux in obese and healthy humans as evaluated by 15N- and 2H3-labeled alanines

    Estimates of plasma alanine flux as measured in humans using L-[15N]-alanine or L-[3,3,3-2H3]alanine were compared by simultaneous intravenous infusion of both tracers. Plasma isotope enrichments were measured by chemical ionization gas chromatography-mass spectrometry. In 16 obese women before and during a hypocaloric diet and in 4 normal men in the postabsorptive and fed states, the fluxes were highly correlated (r2 = 0.93) although plasma alanine flux with the 2H tracer was two to three times greater than that obtained with [15N]alanine. The fluxes decreased with the hypocaloric diet in obese subjects and increased during the fed state in healthy adults. Thus, although the estimates of alanine flux differed according to the tracer used, both appear to give equivalent information about changes in alanine kinetics induced by the nutritional conditions examined

  12. Utilization of 15N-labelled urea in laying hens. 7

    3 colostomized laying hybrids received 1% 15N-labelled urea with 96.06 atom-% 15N excess (15N') with a commercial ration over a period of 6 days. After the application of the same ration with unlabelled urea on the following 2 days the animals were butchered. In the muscles of breast, legs and heart, the labelling of total nitrogen and the incorporation of urea 15N' into 15 amino acids of the 3 different kinds of muscles were ascertained. On average, significant differences could be ascertained between the atom-% 15N of the muscles was 0.25 and 0.34 atom-%, resp.; that of the cardial proteins 0.71 atom-% 15N'. The incorporation of urea 15N into the basic amino acids is low and varies both between the kinds of muscles and between the amino acids. On average the highest level of labelling was found among the essential amino acids valine, isoleucine and leucine; the average atom-% 15N' for the muscles of the breast is 0.13, of the leg 0.17, and of the heart 0.27; the 15N' quota of branched Chain amino acids in the total 15N' of the respective muscle is accordingly 6.0%, 5.0% and 4.5%. The non-essential amino acids, particularly glutamic acid, are more highly labelled in the muscles than the essential ones. A 15N' for glutamic acid of 0.24 atom-% in the breast muscles, of 0.27 atom-% in those of the legs and of 0.64 atom-% in the heart muscle could be detected. The average quota of the 15N' of these acid amino acids in the 15N' for breast, leg and heart muscles is 7.4, 6.2 and 6.7, resp. The quota of the 15N' in the 6 non-essential amino acids in the total 15N' in all 3 kinds of muscles is approximately two thirds and in the 9 essential ones one third of the total 15N'. Although the results show that there is a certain incorporation of 15N' from urea into the amino acids of the muscle proteins, their contribution to meeting the demands is irrelevant. (author)

  13. The Use Of 15N in the Study of Nitrogen Uptake and Metabolism in Plants

    Some forty years ago Mattson attempted to represent soil solutions as ionic states. Later on, he further developed his theory with the aid of the latest achievements in physical chemistry. In 1955 Schoffield applied chemical thermodynamics to make the interrelations between the solid and liquid phases of the soil even more precise. Nitrogen occupies a special position among the plant nutrients. The greatest success in nitrogen uptake and metabolism studies, however, has been achieved only recently after the development of isotope techniques. The study of nitrogen metabolism using isotope techniques has been carried out for some years at the N. Poushkarov Institute of Soil Science using optical methods of isotope detection. Certain of the results obtained recently point to the great opportunities offered by the use of the optical method. Greenhouse and field experiments were carried out with wheat, oats and lucerne. Ammonium sulphate with 11.50 at.%, 15N,andurea 5.55 at % were used as sources of nitrogen. Depending on the conditions, the nitrogen introduced with fertilizers was utilized by the plants in amounts ranging from 47 to 56% in the greenhouses, and from 38 to 45% m the field. It was established that the soil was the source of nearly half the nitrogen of the plants. Fertilized plants took up more of the soil nitrogen than the unfertilized plants. The nitrogen introduced into the soil was found in all fractions of the plants after 24 h and was in the non-protein organic nitrogen, constitution proteins, chlorophyll and reserve proteins of the plants. The highest amounts of 15N were found in the following free amino acids: arginine, histidine, lysine and the amide aspargine. In the bound amino acids, alanine, threonine, serine and glycine were highest in 15N. Phosphorus application increased the amounts of nitrogen in the amino acids. It was established that nitrogen turnover was greatest in chlorophyll and the constitution proteins. In the study of the quality

  14. Protein backbone motions viewed by intraresidue and sequential HN-Hα residual dipolar couplings

    Triple resonance E.COSY-based techniques were used to measure intra-residue and sequential HN-Hα residual dipolar couplings (RDCs) for the third IgG-binding domain of protein G (GB3), aligned in Pf1 medium. Measurements closely correlate with values predicted on the basis of an NMR structure, previously determined on the basis of a large number of one-bond backbone RDCs measured in five alignment media. However, in particular the sequential HN-Hα RDCs are smaller than predicted for a static structure, suggesting a degree of motion for these internuclear vectors that exceeds that of the backbone amide N-H vectors. Of all experimentally determined GB3 structures available, the best correlation between experimental 1H-1H couplings is observed for a GB3 ensemble, previously derived to generate a realistic picture of the conformational space sampled by GB3 (Clore and Schwieters, J Mol Biol 355:879-886, 2006). However, for both NMR and X-ray-derived structures the 1H-1H couplings are found to be systematically smaller than expected on the basis of alignment tensors derived from 15N-1H amide RDCs, assuming librationally corrected N-H bond lengths of 1.041 A

  15. Acetylene inhibition of N2O reduction in laboratory soil and groundwater denitrification assays: evaluation by 15N tracer and 15N site preference of N2O

    Weymann, Daniel; Well, Reinhard; Lewicka-Szczebak, Dominika; Rohe, Lena

    2013-01-01

    Acetylene inhibition of N2O reduction in laboratory soil and groundwaterdenitrification assays: evaluation by 15N tracer and 15N site preference ofN2ODaniel Weymann (1), Reinhard Well (2), Dominika Lewicka-Szczebak (2,3), and Rohe Lena (2)(1) Forschungszentrum Juelich, Agrosphere Institute (IBG-3), Juelich, Germany (), (2)Thünen-Institute of Climate-Smart Agriculture, Braunschweig, Germany, (3) University of Wroclaw, PolandThe measurement of denitrification in soils and...

  16. Investigation into endogenous N metabolism in 15N-labelled pigs. 1

    4 male castrated pigs (55-65 kg) either received a wheat-fish meal diet (1 and 2) or a wheat-horse bean diet (3 and 4) without straw meal supplement (1 and 3) or with a supplement of 20% dry matter (2 and 4). In order to investigate whether a 15N labelling of the pigs is also possible with a protein excess in the ration, the animals received 24.8 g (1 and 2) and 11.6 g crude protein/kg/sup 0.75/ live weight (3 and 4). During a 10-day 15N-labelling 385 mg 15N excess (15N') per kg/sup 0.75/ were applied with 15N labelling the following quotas of the applied 15N amount were incorporated: 1 = 10.2%, 2 = 7.2%, 3 = 18.7%, 4 = 14.4%. 15N excretion in both TCA fractions of feces showed a highly significant positive correlation to the increasing content of crude fibre in the 4 diets. The immediate 15N incorporation into the TCA-precipitable fraction of feces proves that 15N enters the large intestine endogenously and serves bacterial protein synthesis. 3 days after the last 15 application the pigs were killed. The values of atom-% 15N' were determined in the TCA-precipitable blood plasma and in the TCA-precipitable fraction of the liver. The other examined organs and tissues showed smaller differences between the test animals. The results show that the 15N labelling of tissues and organs of pigs is also possible at a high level of protein supply by means of an oral application of [15N] ammonia salts. (author)

  17. Simultaneous NMR assignment of backbone and side chain amides in large proteins with IS-TROSY

    A new strategy for the simultaneous NMR assignment of both backbone and side chain amides in large proteins with isotopomer-selective transverse-relaxation-optimized spectroscopy (IS-TROSY) is reported. The method considers aspects of both the NMR sample preparation and the experimental design. First, the protein is dissolved in a buffer with 50%H2O/50%D2O in order to promote the population of semideuterated NHD isotopomers in side chain amides of Asn/Gln residues. Second, a 13C'-coupled 2D 15N-1H IS-TROSY spectrum provides a stereospecific distinction between the geminal protons in the E and Z configurations of the carboxyamide group. Third, a suite of IS-TROSY-based triple-resonance NMR experiments, e.g. 3D IS-TROSY-HNCA and 3D IS-TROSY-HNCACB, are designed to correlate aliphatic carbon atoms with backbone amides and, for Asn/Gln residues, at the same time with side chain amides. The NMR assignment procedure is similar to that for small proteins using conventional 3D HNCA/3D HNCACB spectra, in which, however, signals from NH2 groups are often very weak or even missing due to the use of broad-band proton decoupling schemes and NOE data have to be used as a remedy. For large proteins, the use of conventional TROSY experiments makes resonances of side chain amides not observable at all. The application of IS-TROSY experiments to the 35-kDa yeast cytosine deaminase has established a complete resonance assignment for the backbone and stereospecific assignment for side chain amides, which otherwise could not be achieved with existing NMR experiments. Thus, the development of IS-TROSY-based method provides new opportunities for the NMR study of important structural and biological roles of carboxyamides and side chain moieties of arginine and lysine residues in large proteins as well as amino moieties in nucleic acids

  18. Direct measurement of the 15N CSA/dipolar relaxation interference from coupled HSQC spectra

    Here we propose a method for the measurement of the 15N CSA/dipolar relaxation interference based on direct comparison of the 15N doublet components observed in a 1H-coupled 1H-15N HSQC-type spectrum. This allows the determination of the cross-correlation rates with no need for correction factors associated with other methods. The signal overlap problem of coupled HSQC spectra is addressed here by using the IPAP scheme (Ottiger et al., 1998). The approach is applied to the B3 domain of protein G to show that the method provides accurate measurements of the 15N CSA/dipolar cross-correlation rates

  19. Investigation of the metabolism of colostomized laying hens with 15N-labelled wheat. 5

    In an experiment with 3 colostomized laying hybrids each animal received 80 g pelleted mixed feed and 40 g 15N-labelled wheat with 20.13 atom-% 15N excess (15N') over a period of four days. On the following four days the hens received rations composed in the same way with unlabelled wheat, however in the tissues and organs of the slaughtered hens 15N' was determined in the total N and the amino acids lysine, histidine and arginine in both the segments of the gastro intestinal tract and in its content. The amount of 15N' stomach, small intestine and colon was 43.7%, 27.2% and 29.1%, respectively. The tissue of the small intestine contained, on an average, the highest 15N' in lysine of all the basic amino acids. It was 0.82 atom-% 15N' for lysine, 0.55% for histidine and 0.63% for arginine. The percentage of the 15N' of the basic amino acids from the corresponding total 15N' amount of the charges was 20.5% in the contents of the gastrointestinal tract, 28.0% in the stomach tissue and in the tissues of the small intestine 24.4% of the cecum 21.5% and of the rectum 25.7%. (author)

  20. Utilization of 15N-labelled urea in laying hens. 6

    3 colostomized laying hybrids received a normal ration containing 1% 15N-labelled urea with 96.06% atom-% 15N excess (15N') over six days. Subsequently the same ration with unlabelled urea was given over 2 days, after which the animals were butchered. In the kidneys the 15N' amounted to 1.1 atom-% and 1.8 atom-% in the liver. The TCA soluble N fraction and the ammonia were more highly labelled than the total N. Lysine, histidine and arginine were lowly labelled in the kidneys. This also applies to the liver with the exception of histidine. In the branch-chained and aromatic amino acids of the liver the 15N' was between 0.2 and 0.3 atom-%. The highest labelling of non-essential amino acids was found in glutamic acid with 0.9 atom-% 15N' and aspartic acid with 1.1 atom-% 15 N'. The evaluation of the amino acid in the liver showed that the 6 non-essential amino acids account for two thirds of the total amino acid 15N' whereas the 9 essential ones account for one third of the amino acid 15N' only. (author)

  1. Effects of growth and change of food on the δ15N in marine fishes

    Information is limited concerning variation of the δ15N with growth in marine organisms and consequently the effect of growth of marine biota on the δ15N is not yet well understood. The δ15N in 26 species of marine fishes taken from Japanese coastal waters together with 4664 stomach contents of these fishes were examined to investigate the effects of food habits and growth on the δ15N. The mean δ15N for two species that fed mainly on large-size fishes and six species that fed mainly on small-size fishes were 14.5±1.0per mille and 12.8±0.7per mille, respectively. For five species that fed mainly on decapod crustaceans, two species that fed mainly on zooplankton, and three species that fed mainly on benthos (mainly Polychaeta), the δ15N were 13.0±0.7, 9.7±0.9, and 12.2±1.2per mille, respectively. The mean δ15N in the species whose prey were mainly fish or decapod crustaceans was about 3-5per mille higher than the species whose prey was mainly zooplankton. Within the four species that shift their food habits with growth to higher trophic level, the δ15N significantly increased with growth in one species (Pacific cod), while not significant increase in the δ15N with growth in the remaining species. (author)

  2. Nitrogen (15N) recovery from ammonium and nitrate applied to the soil by sugar cane

    An experiment was developed in a field aimed to compare the recovery of the ammonium-15 N and nitrate-15 N by the sugar cane plants harvested mechanically without burning. A rate of 70 kg ha-1 of N was applied as ammonium nitrate, in strip, onto cultural residues. Two lineal meters micropots were used. They received the fertilizer labeled with 15 N. Two treatments were established using labeled ammonium (NH4+-15 N) or nitrate (NO3-15 N). Two months after fertilization, four samples of the aerial part (two lineal meters) for treatment in the portions that did not receive the fertilizer-15 N, were taken in order to evaluated the fitomass production (Mg ha-1) and N-total accumulated (kg ha-1). This evaluation was repeated every two months up to complete five of them. Two leaves (leaves with 3 deg C visible auricle) were collected from plants that were in a middle of the micropots (15 N) and in corresponding positions in the adjacent rows, to evaluated the concentration of 15 N. There was a larger absorption of the nitrate-N (30.5%) than of the ammonium-N (21.2%). On the other hand, in the soil the results showed larger ammonium-15 N residual effect concentration, probably due to microorganism immobilization. (author)

  3. High Performance Infiltrated Backbones for Cathode-Supported SOFC's

    Gil, Vanesa; Kammer Hansen, Kent

    2014-01-01

    A four-step infiltration method has been developed to infiltrate La0.75Sr0.25MnO3+δ (LSM25) nanoparticles into porous structures (YSZ or LSM-YSZ backbones). The pore size distribution in the backbones is obtained either by using PMMA and/or graphites as pore formers or by leaching treatment of...

  4. Determination of Protein Backbone Structures from Residual Dipolar Couplings

    Prestegard, J H; Mayer, K. L.; Valafar, H.; Benison, G. C.

    2005-01-01

    There are a number of circumstances where a focus on determination of the backbone structure of a protein, as opposed to a complete all-atom structure, may be appropriate. This is particularly the case for structures determined as a part of a structural genomics initiative where computational modeling of many sequentially related structures from the backbone of a single family representative is anti...

  5. Free backbone carbonyls mediate rhodopsin activation.

    Kimata, Naoki; Pope, Andreyah; Sanchez-Reyes, Omar B; Eilers, Markus; Opefi, Chikwado A; Ziliox, Martine; Reeves, Philip J; Smith, Steven O

    2016-08-01

    Conserved prolines in the transmembrane helices of G-protein-coupled receptors (GPCRs) are often considered to function as hinges that divide the helix into two segments capable of independent motion. Depending on their potential to hydrogen-bond, the free C=O groups associated with these prolines can facilitate conformational flexibility, conformational switching or stabilization of the receptor structure. To address the role of conserved prolines in family A GPCRs through solid-state NMR spectroscopy, we focus on bovine rhodopsin, a GPCR in the visual receptor subfamily. The free backbone C=O groups on helices H5 and H7 stabilize the inactive rhodopsin structure through hydrogen-bonds to residues on adjacent helices. In response to light-induced isomerization of the retinal chromophore, hydrogen-bonding interactions involving these C=O groups are released, thus facilitating repacking of H5 and H7 onto the transmembrane core of the receptor. These results provide insights into the multiple structural and functional roles of prolines in membrane proteins. PMID:27376589

  6. A data acquisition backbone core library

    For the new experiments at FAIR new concepts of data acquisition systems have to be developed like the distribution of self-triggered, time stamped data streams over high performance networks for event building. The data acquisition backbone core (DABC) is a general purpose software framework designed for the implementation of such data acquisition systems. It provides the event building over networks like InfiniBand or Gigabit Ethernet. All kinds of data channels (front-end systems) are supported by program plug-ins into functional components of DABC like data input, combiner, scheduler, event builder, analysis and storage components. Commands and parameters of DABC and its application plug-ins are published by DIM servers. A Java based Graphical User Interface provides the dynamic control and visualization of these components. Application specific GUIs can be added. After a testing phase, DABC can be used to develop high performance data acquisition systems. Besides that DABC will be used for the implementation of various test beds needed for the final design of data acquisition systems at FAIR like detector tests, readout components test, and data flow investigations

  7. Factors Controlling the Stable Nitrogen Isotopic Composition (δ15N of Lipids in Marine Animals.

    Elisabeth Svensson

    Full Text Available Lipid extraction of biomass prior to stable isotope analysis is known to cause variable changes in the stable nitrogen isotopic composition (δ15N of residual biomass. However, the underlying factors causing these changes are not yet clear. Here we address this issue by comparing the δ15N of bulk and residual biomass of several marine animal tissues (fish, crab, cockle, oyster, and polychaete, as well as the δ15N of the extracted lipids. As observed previously, lipid extraction led to a variable offset in δ15N of biomass (differences ranging from -2.3 to +1.8 ‰. Importantly, the total lipid extract (TLE was highly depleted in 15N compared to bulk biomass, and also highly variable (differences ranging from -14 to +0.7 ‰. The TLE consisted mainly of phosphatidylcholines, a group of lipids with one nitrogen atom in the headgroup. To elucidate the cause for the 15N-depletion in the TLE, the δ15N of amino acids was determined, including serine because it is one of the main sources of nitrogen to N-containing lipids. Serine δ15N values differed by -7 to +2 ‰ from bulk biomass δ15N, and correlated well with the 15N depletion in TLEs. On average, serine was less depleted (-3‰ than the TLE (-7 ‰, possibly due to fractionation during biosynthesis of N-containing headgroups, or that other nitrogen-containing compounds, such as urea and choline, or recycled nitrogen contribute to the nitrogen isotopic composition of the TLE. The depletion in 15N of the TLE relative to biomass increased with the trophic level of the organisms.

  8. Nitrogen-15 labeled 5S RNA. Identification of uridine base pairs in Escherichia coli 5S RNA by 1H-15N multiple quantum NMR

    Escherichia coli 5S RNA labeled with 15N at N3 of the uridines was isolated from the Sφ-187 uracil auxotroph grown on a minimal medium supplemented with [3-15N]uracil. 1H-15N multiple quantum filtered and 2D chemical shift correlated spectra gave resonances for the uridine imino 1H-15N units whose protons were exchanging slowly with solvent. Peaks with 1H/15N shifts at 11.6/154.8, 11.7/155.0, 11.8/155.5, 12.1/155.0, and 12.2/155.0 ppm were assigned to GU interactions. Two labile high-field AU resonances at 12.6/156.8 and 12.8/157.3 ppm typical of Au pairs in a shielded environment at the end of a helix were seen. Intense AU signals were also found at 13.4/158.5 and 13.6/159.2 ppm where 1H-15N units in normal Watson-Crick pairs resonate. 1H resonances at 10.6 and 13.8 ppm were too weak, presumably because of exchange with water, to give peaks in chemical shift correlated spectra. 1H chemical shifts suggest that the resonance at 13.8 ppm represents a labile AU pair, while the resonance at 10.6 ppm is typical of a tertiary interaction between U and a tightly bound water or a phosphate residue. The NMR data are consistent with proposed secondary structures for 5S RNA

  9. Backbone flexibility in protein design theory and experiment

    Su, Alyce

    The role of backbone flexibility in protein design was studied. First, the effect of explicit backbone motion on the selection of amino acids in protein design was assessed in the core of the streptococcal protein Gβ1 domain (Gβ1). Concerted backbone motion was introduced by varying Gβ1's supersecondary structure parameter values. The stability and structural flexibility of seven of the redesigned proteins were determined experimentally. Core variants containing as many as six of ten possible mutations retained native-like properties. This result demonstrates that backbone flexibility can be combined with amino acid side-chain selection and that the selection algorithm is sufficiently robust to tolerate perturbations as large as 15% of the native parameter values. Second, a general, quantitative design method for computing de novo backbone templates was developed. The method had to compute atomic resolution backbones compatible with the atomistic sequence selection algorithm we were using and it had to be applicable to all protein motifs. We again developed a method that uses super-secondary structure parameters to determine the orientation among secondary structural elements, given a target protein fold. Possible backbone arrangements were screened using a cost function which evaluates core packing, hydrogen bonding, loop closure, and backbone torsional geometry. Given a specified number of residues for each secondary structural element, a family of optimal configurations was found. We chose three motifs to test our method (ββα, βαβ, and αα) since their combination could be used to approximate most possible backbone fold. The best structure found for the ββα motif is similar to a zinc finger, and the best structure for the ββα motif is similar to a segment of a β-barrel. The backbone obtained for the αα motif resembles minimized protein A. Last, our backbone design method was evaluated by testing the thermal stability and structural properties

  10. Identical repeated backbone of the human genome

    Gonzaga-Jauregui Claudia

    2010-01-01

    Full Text Available Abstract Background Identical sequences with a minimal length of about 300 base pairs (bp have been involved in the generation of various meiotic/mitotic genomic rearrangements through non-allelic homologous recombination (NAHR events. Genomic disorders and structural variation, together with gene remodelling processes have been associated with many of these rearrangements. Based on these observations, we identified and integrated all the 100% identical repeats of at least 300 bp in the NCBI version 36.2 human genome reference assembly into non-overlapping regions, thus defining the Identical Repeated Backbone (IRB of the reference human genome. Results The IRB sequences are distributed all over the genome in 66,600 regions, which correspond to ~2% of the total NCBI human genome reference assembly. Important structural and functional elements such as common repeats, segmental duplications, and genes are contained in the IRB. About 80% of the IRB bp overlap with known copy-number variants (CNVs. By analyzing the genes embedded in the IRB, we were able to detect some identical genes not previously included in the Ensembl release 50 annotation of human genes. In addition, we found evidence of IRB gene copy-number polymorphisms in raw sequence reads of two diploid sequenced genomes. Conclusions In general, the IRB offers new insight into the complex organization of the identical repeated sequences of the human genome. It provides an accurate map of potential NAHR sites which could be used in targeting the study of novel CNVs, predicting DNA copy-number variation in newly sequenced genomes, and improve genome annotation.

  11. Enhanced conformational space sampling improves the prediction of chemical shifts in proteins.

    Markwick, Phineus R L; Cervantes, Carla F; Abel, Barrett L; Komives, Elizabeth A; Blackledge, Martin; McCammon, J Andrew

    2010-02-01

    A biased-potential molecular dynamics simulation method, accelerated molecular dynamics (AMD), was combined with the chemical shift prediction algorithm SHIFTX to calculate (1)H(N), (15)N, (13)Calpha, (13)Cbeta, and (13)C' chemical shifts of the ankyrin repeat protein IkappaBalpha (residues 67-206), the primary inhibitor of nuclear factor kappa-B (NF-kappaB). Free-energy-weighted molecular ensembles were generated over a range of acceleration levels, affording systematic enhancement of the conformational space sampling of the protein. We have found that the predicted chemical shifts, particularly for the (15)N, (13)Calpha, and (13)Cbeta nuclei, improve substantially with enhanced conformational space sampling up to an optimal acceleration level. Significant improvement in the predicted chemical shift data coincides with those regions of the protein that exhibit backbone dynamics on longer time scales. Interestingly, the optimal acceleration level for reproduction of the chemical shift data has previously been shown to best reproduce the experimental residual dipolar coupling (RDC) data for this system, as both chemical shift data and RDCs report on an ensemble and time average in the millisecond range. PMID:20063881

  12. Turnover of 15N labelled nitrate with special emphasis on denitrification in the field

    This study establishes a mass balance for 15N-labelled nitrate added to soil planted with a nitrogen-fixing crop (pea) and a non-fixing crop (barley). The results indicate that 15N unaccounted for in a mass balance is not necessarily lost by denitrification. Processes such as volatilization of ammonia should also be considered. 1 fig

  13. Synthesis and isotope-ratio analysis of methyl nitrite-15N

    Methyl nitrite-15N was synthesised on a 0.1 mole scale by the esterification of methanol by aqueous H15NO2. The method is simple and efficient, and provides analytically pure CH3O15NO. A method for determining the 15N enrichment of CH3O15NO is described. (author)

  14. Improvement of differential diagnostics in pseudohermaphroditismus masculinus by means of 15N-labelled amino acids

    In 7 children with male hermaphroditism the N retention test was performed using 15N-glycine (13.5 mg/kg body weight). On testosterone therapy the protein synthesis rate increased significantly while there was a significant decrease in the cumulative 15N excretion

  15. Increased Plant Uptake of Nitrogen from 15N Depleted Fertilizer Using Plant Growth-Promoting Rhizobacteria

    The techniques of 15N isotope have been very useful for determining the behavior and fate of N in soil, including the use efficiency of applied N fertilizers by plants. Our objective in this study was to use 15N isotope techniques to demonstrate that a model plant growth-promoting rhizobacteria (PGP...

  16. Application of 15N amino acid absorption in chronic enteropathy and hepatic diseases in infants

    The aim of this study was to estimate malabsorption status in humans using a 15N stable isotope tracer technique. [15N]-glycine, 98.98 atom %, was synthesized in our institute and was administered orally as a single bolus dose to twelve patients. Six of the 12 subjects studied were healthy and 6 were suspected of having malabsorption. Blood, urine and faecal samples were obtained, proteins in the samples were precipitated with sulphosalicylic acid (5%), the eluate was purified with Dowex 50W-X8 (40mm x 2mm column), and derivatised to form the trifluoroacetyl-butyl esters using standard techniques. Gas chromatographic separation was performed on a glass column 2m X 3mm i.d. packed with EGA 1% on Chromosorb W AW 80-100 mesh. An isotope dilution GC/MS method and Kjeldahl digestion followed by MS analysis of nitrogen gas was performed. 15N isotopomer was used as internal standard. [15N]-Gly elimination in faeces was compared with total 15N elimination in faeces to distinguish artefacts caused by intestinal bacteria. Significant differences in the amount of [15N]-Gly eliminated in urine and faeces between malabsorption and control patients were obtained. It was concluded that more emphasis should be given to the faeces data than to urine because 15N elimination in urine is competitive with 15N incorporation into protein. 12 refs, 4 figs, 4 tabs

  17. Utilization of 15N-labelled urea in laying hens. 8

    3 colostomized laying hybrids received orally with a conventional ration 1% urea with 96.06 atom-% 15N excess (15N') over a period of 6 days. In the period of the experiment every hen consumed 2.87 g 15N'. After another 2 days, on which they received conventional feed urea, the animals were butchered. 15N' was determined in the total N and in 15 amino acids of the oviduct. Of the 15 amino acids the labelling of glutamic acid, glycine and serine was highest and on average amounted to 0.80, 0.66 and 0.67 atom-% 15N', resp. In lysine and arginine only 0.10 and 0.11 atom-% 15N' could be detected. The amino acid N with natural isotopic frequency amounted to a quarter for the basic amino acids, a tenth for the branched chain ones and for the non-essential ones (glutamic acid, aspartic acid, serine, glycine, alanine, proline) a third of the total oviduct 14N. The average quota of 15N' is only 3.6%, that of the branched chain amino acids 4.5 and that of the non-essential ones 21.1%. Consequently, the 15N' of the urea is mainly used for the synthesis of the non-essential amino acids of the oviduct. (author)

  18. Utilization of 15N-labelled urea in laying hens. 2

    In an N metabolism experiment 3 colostomized laying hybrids received 2870 mg 15N excess (15N') per animal in 6 days in the form of urea with their conventional feed rations. During the 8-day experiment the 21 eggs laid were separated into egg-shell, white of egg and yolk. Weight, N content and 15N' of the individual fractions of the eggs were determined. On an average 4.6% of the heavy nitrogen was in the egg-shells, 50% in the white of egg and 45.5% in the yolk. 2.8%, 4.5% and 5.5% (hens 1 - 3) of the 15N' consumed were detected in the eggs. The maximum 15N' output in the white of egg was reached on the 6th day, whereas 15N' output in the yolk showed a nearly linear increase in the time of the experiment. The results show that labelled nitrogen from urea is incorporated into the egg to a lower degree than after the feeding of 15N-labelled proteins and that the development of its incorporation into the white of egg and the yolk differ from that after the feeding of 15N-labelled native proteins. (author)

  19. Disturbance and topography shape nitrogen availability and δ15N over long-term forest succession

    Forest disturbance and long-term succession can promote open N cycling that increases N loss and soil δ15N values. We examined soil and foliar patterns in N and δ15N, and soil N mineralization, across a topographically complex montane forest landscape influenced by human logging ...

  20. Global Fold of Human Cannabinoid Type 2 Receptor Probed by Solid-State 13C-, 15N-MAS NMR and Molecular Dynamics Simulations

    Kimura, Tomohiro; Vukoti, Krishna; Lynch, Diane L.; Hurst, Dow P.; Grossfield, Alan; Pitman, Michael C.; Reggio, Patricia H.; Yeliseev, Alexei A.; Gawrisch, Klaus

    2013-01-01

    The global fold of human cannabinoid type 2 (CB2) receptor in the agonist-bound active state in lipid bilayers was investigated by solid-state 13C- and 15N magic-angle spinning (MAS) NMR, in combination with chemical-shift prediction from a structural model of the receptor obtained by microsecond-long molecular dynamics (MD) simulations. Uniformly 13C-, and 15N-labeled CB2 receptor was expressed in milligram quantities by bacterial fermentation, purified, and functionally reconstituted into l...

  1. Efficient Algorithms for Extension of Mobile Backbone Networks

    Eswaramoorthi. R

    2012-03-01

    Full Text Available Network wide communication is an essential criterion for all wireless sensor networks, to transmit the collected data from environment to base station (sink node in an efficient way. The wide network coverage is provided by constructing Mobile Backbone Networks (MBN, which are dynamic networks. These networks have two types of nodes. They are Mobile backbone nodes and Regular nodes. The Mobile backbone nodes have superior mobility and communication capability than regular nodes. All the information needs to be routed through mobile backbone nodes to regular nodes. The communication between clusters is done through backbone node so that transmission overhead is less. In this paper, we are mainly concentrates on throughput optimization and assigning new regular nodes. First the throughput range is calculated for each cluster, and then data packets are transmitted in such a way that the calculated range of throughput for each cluster is satisfied. The number of regular nodes that can be successfully assigned to mobile backbone nodes can be improved by means of adopting network design formulation technique. In case of any failure of mobile backbone node ,new cluster head is elected based on high energy first (HEF algorithm, where the residual energy of the nodes are considered for election.

  2. Radiation safety system (RSS) backbones: Design, engineering, fabrication and installation

    Wilmarth, J.E.; Sturrock, J.C.; Gallegos, F.R.

    1998-12-01

    The Radiation Safety System (RSS) Backbones are part of an electrical/electronic/mechanical system insuring safe access and exclusion of personnel to areas at the Los Alamos Neutron Science Center (LANSCE) accelerator. The RSS Backbones control the safety fusible beam plugs which terminate transmission of accelerated ion beams in response to predefined conditions. Any beam or access fault of the backbone inputs will cause insertion of the beam plugs in the low energy beam transport. The Backbones serve the function of tying the beam plugs to the access control systems, beam spill monitoring systems and current-level limiting systems. In some ways the Backbones may be thought of as a spinal column with beam plugs at the head and nerve centers along the spinal column. The two Linac Backbone segments and experimental area segments form a continuous cable plant over 3,500 feet from beam plugs to the tip on the longest tail. The Backbones were installed in compliance with current safety standards, such as installation of the two segments in separate conduits or tray. Monitoring for ground-faults and input wiring verification was an added enhancement to the system. The system has the capability to be tested remotely.

  3. Radiation safety system (RSS) backbones: Design, engineering, fabrication and installation

    The Radiation Safety System (RSS) Backbones are part of an electrical/electronic/mechanical system insuring safe access and exclusion of personnel to areas at the Los Alamos Neutron Science Center (LANSCE) accelerator. The RSS Backbones control the safety fusible beam plugs which terminate transmission of accelerated ion beams in response to predefined conditions. Any beam or access fault of the backbone inputs will cause insertion of the beam plugs in the low energy beam transport. The Backbones serve the function of tying the beam plugs to the access control systems, beam spill monitoring systems and current-level limiting systems. In some ways the Backbones may be thought of as a spinal column with beam plugs at the head and nerve centers along the spinal column. The two Linac Backbone segments and experimental area segments form a continuous cable plant over 3,500 feet from beam plugs to the tip on the longest tail. The Backbones were installed in compliance with current safety standards, such as installation of the two segments in separate conduits or tray. Monitoring for ground-faults and input wiring verification was an added enhancement to the system. The system has the capability to be tested remotely

  4. Utilization of fertilizer and stored nitrogen by asparagus and kiwifruit estimated using 15N

    The efficiency of recovery of 15N enriched nitrogen fertilizer was examined in field trials on two contrasting mature perennial crops: a vegetable (asparagus) and a woody deciduous vine (kiwifruit). In the asparagus experiment, 50 kg N/ha were applied either prior to fern growth (early summer) or pre-harvest (early spring). In the former treatment, 15N uptake was rapid during the period of fern growth (summer and autumn) and by early winter most 15N had been stored in crown and root material. In contrast, uptake of 15N applied pre-harvest was slow, indicating that most of the N for spear production was from remobilization of stored N. Removal of added 15N in produce over two harvest years was small. 8 refs, 3 tabs

  5. Syntheses of 15N-labeled pre-queuosine nucleobase derivatives

    Jasmin Levic

    2014-08-01

    Full Text Available Pre-queuosine or queuine (preQ1 is a guanine derivative that is involved in the biosynthetic pathway of the hypermodified tRNA nucleoside queuosine (Que. The core structure of preQ1 is represented by 7-(aminomethyl-7-deazaguanine (preQ1 base. Here, we report the synthesis of three preQ1 base derivatives with complementary 15N-labeling patterns, utilizing [15N]-KCN, [15N]-phthalimide, and [15N3]-guanidine as cost-affordable 15N sources. Such derivatives are required to explore the binding process of the preQ1 base to RNA targets using advanced NMR spectroscopic methods. PreQ1 base specifically binds to bacterial mRNA domains and thereby regulates genes that are required for queuosine biosynthesis.

  6. Standardized 15N tracer methods for the evaluation of the plasma protein turnover in clinical practice. 1

    Methods for quantitative isolation of plasma proteins or groups of proteins (total plasma or serum proteins, fibrin, total globulines, α, β, γ-globolines, albumin) are described based on combination of chromatography with precipitation and extraction techniques. These methods are adapted to the special requirements of 15N analysis. They can be performed in clinic-chemical standard laboratories without special apparatuses or devices. The described procedures are the biochemico-analytical basis for the quantitative evaluation of tracer kinetics data by means of mathematic modelling. (author)

  7. Using a macroalgal δ15N bioassay to detect cruise ship waste water effluent inputs

    Highlights: → Green macroalgae exposed to nutrient solutions exhibited changes in tissue 15N signatures. → Macroalgae exhibited no fractionation with NO3 and slight fractionation with NH4. → Algae exposed to cruise ship waste water had increased tissue δ15N indicating a heavy N source. → Field bioassays exhibited decreased δ15N indicating isotopically light riverine δ15N-NO3 was likely the dominant N source. → Algal bioassays could not detect a δ15N cruise ship waste water signal in this system. - Abstract: Green macroalgae bioassays were used to determine if the δ15N signature of cruise ship waste water effluent (CSWWE) could be detected in a small harbor. Opportunistic green macroalgae (Ulva spp.) were collected, cultured under nutrient depleted conditions and characterized with regard to N content and δ15N. Samples of algae were used in controlled incubations to evaluate the direction of isotope shift from exposure to CSWWE. Algae samples exposed to CSWWE exhibited an increase of 1-2.5 per mille in δ15N values indicating that the CSWWE had an enriched isotope signature. In contrast, algae samples exposed to field conditions exhibited a significant decrease in the observed δ15N indicating that a light N source was used. Isotopically light, riverine nitrogen derived from N2-fixing trees in the watershed may be a N source utilized by algae. These experiments indicate that the δ15N CSWWE signature was not detectable under the CSWWE loading conditions of this experiment.

  8. Utilization of 15N-labelled urea in laying hens. 9

    For studying the incorporation of the 15N labelled urea into individual organs and tissues 3 colostomized laying hens were butchered after they had received 1% urea (96.06 atom-% 15N excess) with a high quality ration over a period of six days and after receiving conventional urea for another two days. Nitrogen and atom-% 15N excess (15N') were determined in the bones, the feathers and the remaining body (skin, lungs and windpipe, head with comb and wattle, lower leg without bones and with skin, pancreas and fatty tissue). In the remaining body the atom-% 15N' was determined in 15 amino acids. The labelling in the remaining body and the bones was approximately the same and averaged 0.37 atom-% 15N'. A significantly lower relative frequency could be detected in the feathers. The lysine of the remaining body contained only 0.04 atom-% 15N', tyrosine 0.06, histidine and arginine 0.07. The phenylalanine and proline molecules were labelled with 0.11 atom-% 15N'. Most 15N' was incorporated in serine and glutamic acid with over 0.30 atom-%. In the six non-essential amino acids out of the 15 amino acids studied, 48.6 of the non-isotopic nitrogen of the total N of the remaining body and 70.7% of the isotopic nitrogen of total 15N' could be detected. Consequently the urea N is mainly used for the synthesis of the non-essential amino acids, with its utilization being very low. (author)

  9. Security in Packet-Switched Land Mobile Radio Backbone Networks

    Thomschutz, Hans Olaf Rutger

    2005-01-01

    Spurred by change in government regulations and to leverage lower-cost technology and services, many land mobile radio (LMR) operators have begun transitioning from circuit-switched to packet-switched backbone networks to handle their future communication needs. Due to the unique demands of packet-switched backbone networks for LMR, it may not be wise to carry over the previously implemented security methods used with circuit-switch systems or to treat an LMR backbone as a regular packet-swit...

  10. Labelling of sewage with 13C and 15N isotopes

    Treatment of sewage water varies with the type and level of technology applied. As a result, sewage sludges vary in composition. In Western Europe, a combination of mechanical, biological, and chemical treatments is commonly applied. The biological treatment of sewage water - the activated sludge process - results in removal of carbon and nitrogen through immobilization in microbes. With strong aeration of the wastewater, energy-rich substrates and nutrients are assimilated by aerobic microbes and a large microbial biomass results. The biomass consists mainly of living microbial cells and components of dying and dead cells, but also of colloidal particles and metal ions bound to the surfaces of the microbes. The organic matter produced during aeration - the biological sludge - is removed by settlement. The biological treatment of wastewater was the starting point for the labelling procedure of sewage sludge. Labelling of waste products with stable tracer isotopes can be done in two ways: (i) labelling of the original material from which wastes are generated, e.g. by labelling of the diet fed to animals; and (ii) labelling during the biological turnover through addition of nitrogen or carbon compounds to wastes. In this study, tracers were added to wastewater during biological treatment

  11. NMR experiments for resonance assignments of 13C, 15N doubly-labeled flexible polypeptides: Application to the human prion protein hPrP(23-230)

    A combination of three heteronuclear three-dimensional NMR experiments tailored for sequential resonance assignments in uniformly 15N, 13C-labeled flexible polypeptide chains is described. The 3D (H)N(CO-TOCSY)NH, 3D (H)CA(CO-TOCSY)NH and 3D (H)CBCA(CO-TOCSY)NH schemes make use of the favorable 15N chemical shift dispersion in unfolded polypeptides, exploit the slow transverse 15N relaxation rates of unfolded polypeptides in high resolution constant-time [1H, 15N]-correlation experiments, and use carbonyl carbon homonuclear isotropic mixing to transfer magnetization sequentially along the amino acid sequence. Practical applications are demonstrated with the 100-residue flexible tail of the recombinant human prion protein, making use of spectral resolution up to 0.6 Hz in the 15N dimension, simultaneous correlation with the two adjacent amino acid residues to overcome problems associated with spectral overlap, and the potential of the presently described experiments to establish nearest-neighbor correlations across proline residues in the amino acid sequence

  12. Detection of (15)NNH+ in L1544: non-LTE modelling of dyazenilium hyperfine line emission and accurate (14)N/(15)N values

    Bizzocchi, Luca; Leonardo, Elvira; Dore, Luca

    2013-01-01

    Samples of pristine Solar System material found in meteorites and interplanetary dust particles are highly enriched in (15)N. Conspicuous nitrogen isotopic anomalies have also been measured in comets, and the (14)N/(15)N abundance ratio of the Earth is itself larger than the recognised pre-solar value by almost a factor of two. Ion--molecules, low-temperature chemical reactions in the proto-solar nebula have been repeatedly indicated as responsible for these (15)N-enhancements. We have searched for (15)N variants of the N2H+ ion in L1544, a prototypical starless cloud core which is one of the best candidate sources for detection owing to its low central core temperature and high CO depletion. The goal is the evaluation of accurate and reliable (14)N/(15)N ratio values for this species in the interstellar gas. A deep integration of the (15)NNH+ (1-0) line at 90.4 GHz has been obtained with the IRAM 30 m telescope. Non-LTE radiative transfer modelling has been performed on the J=1-0 emissions of the parent and ...

  13. Variable δ15N Diet-Tissue Discrimination Factors among Sharks: Implications for Trophic Position, Diet and Food Web Models

    Olin, Jill A.; Hussey, Nigel E.; Alice Grgicak-Mannion; Mark W Fritts; Wintner, Sabine P.; Fisk, Aaron T.

    2013-01-01

    The application of stable isotopes to characterize the complexities of a species foraging behavior and trophic relationships is dependent on assumptions of δ(15)N diet-tissue discrimination factors (∆(15)N). As ∆(15)N values have been experimentally shown to vary amongst consumers, tissues and diet composition, resolving appropriate species-specific ∆(15)N values can be complex. Given the logistical and ethical challenges of controlled feeding experiments for determining ∆(15)N values for lar...

  14. NMR characterization of structure, backbone dynamics, and glutathione binding of the human macrophage migration inhibitory factor (MIF).

    Mühlhahn, P; Bernhagen, J; Czisch, M; Georgescu, J; Renner, C; Ross, A; Bucala, R; Holak, T A

    1996-10-01

    Human macrophage migration inhibitory factor is a 114 amino acid protein that belongs to the family of immunologic cytokines. Assignments of 1H, 15N, and 13C resonances have enabled the determination of the secondary structure of the protein, which consists of two alpha-helices (residues 18-31 and 89-72) and a central four-stranded beta-sheet. In the beta-sheet, two parallel beta-sheets are connected in an antiparallel sense. From the total of three cysteines present in the primary structure of MIF, none was found to form disulfide bridges. 1H-15N heteronuclear T1, T2, and steady-state NOE measurements indicate that the backbone of MIF exists in a rigid structure of limited conformational flexibility (on the nanosecond to picosecond time scale). Several residues located in the loop regions and at the N termini of two helices exhibit internal motions on the 1-3 ns time scale. The capacity to bind glutathione was investigated by titration of a uniform 15N-labeled sample and led us to conclude that MIF has, at best, very low affinity for glutathione. PMID:8897610

  15. Nitrogen fertilizer (15N leaching in a central pivot fertigated coffee crop

    Rafael Pivotto Bortolotto

    2012-08-01

    Full Text Available Nitrogen has a complex dynamics in the soil-plant-atmosphere system. N fertilizers are subject to chemical and microbial transformations in soils that can result in significant losses. Considering the cost of fertilizers, the adoption of good management practices like fertigation could improve the N use efficiency by crops. Water balances (WB were applied to evaluate fertilizer N leaching using 15N labeled urea in west Bahia, Brazil. Three scenarios (2008/2009 were established: i rainfall + irrigation the full year, ii rainfall only; and iii rainfall + irrigation only in the dry season. The water excess was considered equal to the deep drainage for the very flat area (runoff = 0 with a water table located several meters below soil surface (capillary rise = 0. The control volume for water balance calculations was the 0 - 1 m soil layer, considering that it involves the active root system. The water drained below 1 m was used to estimate fertilizer N leaching losses. WB calculations used the mathematic model of Penman-Monteith for evapotranspiration, considering the crop coefficient equal to unity. The high N application rate associated to the high rainfall plus irrigation was found to be the main cause for leaching, which values were 14.7 and 104.5 kg ha-1 for the rates 400 and 800 kg ha-1 of N, corresponding to 3.7 and 13.1 % of the applied fertilizer, respectively.

  16. Bromine recovery in residual solutions generated in the 15 N isotopic determination methodology (Rittenberg, 1946)

    The isotopic determination of 15 N (Rittenberg, 1946) is a methodology used in the Laboratory of Isotope Stable (CENA/USP). In this procedure, in the oxidation of nitrogen species for N2, solution of Li Br O is used, generating as residue 50 L y-1 of solution contends Li Br and Li Br O. Seeking to recover the bromine contained in that residue, very toxic substance, a special line was built composed by reaction balloons (1 and 2 liters), addition funnel, gas flow regulator and connections in glass. In the system proposed, after the acidification (sulfuric acid) of the alkaline residual solution, the liberated bromine (Br2) it was then dragged by flow of nitrogen and reacted with solution of LiOH. That reaction facilitated the production of Li Br O in solution (Efficiency = 82±2%), that was reused later on same analytic procedure. The high cost of the liquid bromine is another attractiveness that corroborates the employment of the developed procedure. They took place isotopic determinations using the recovered solutions and prepared, and the observed values didn't show statistical difference (T test of Student). The presented procedure is part of the Management Program of Chemical Residues of CENA/USP, which seeks to destine the residues of responsibility of the institution appropriately, forming professionals to the practices of environmental management. (author)

  17. δ15N of seagrass leaves for monitoring anthropogenic nutrient increases in coral reef ecosystems

    In a coral reef environment, a slight increase in dissolved inorganic nitrogen (DIN;≥1.0 μM) can alter the ecosystem via macroalgal blooms. We collected seagrass leaves from the tropical and subtropical Pacific Ocean in five countries and examined the interactions between nutrient concentrations (C, N, P), molar ratios of nutrients, and δ15N to find a possible indicator of the DIN conditions. Within most sites, the concentrations of nutrients and their molar ratios showed large variations owing to species-specific values. On the other hand, almost identical δ15N values were found in seagrass leaves of several species at each site. The correlations between δ15N and nutrient concentrations and between δ15N and molar ratios of nutrients suggested that nutrient availability did not affect the δ15N value of seagrass leaves by altering the physiological condition of the plants. Increases in δ15N of seagrass leaves mostly matched increases in DIN concentrations in the bottom water. We suggest that δ15N in seagrass leaves can be a good tool to monitor time-integrated decrease/increase of DIN concentrations at a site, both in the water column and the interstitial water

  18. 15N-labeled nitrogen from green manure and ammonium sulfate utilization by the sugarcane ratoon

    Legumes as green manure are alternative sources of nitrogen (N) for crops and can supplement or even replace mineral nitrogen fertilization due to their potential for biological nitrogen fixation (BNF). The utilization of nitrogen by sugarcane (Saccharum spp.) fertilized with sunn hemp (Crotalaria juncea L.) and ammonium sulfate (AS) was evaluated using the 15N tracer technique. N was added at the rate of 196 and 70 kg ha-1 as 15N-labeled sunn hemp green manure (SH) and as ammonium sulfate (AS), respectively. Treatments were: (I) Control; (II) AS15N; (III) SH15N + AS; (IV) SH15N; and (V) AS15N + SH. Sugarcane was cultivated for five years and was harvested three times. 15N recovery was evaluated in the two first harvests. In the sum of the three harvests, the highest stalk yields were obtained with a combination of green manure and inorganic N fertilizer; however, in the second cutting the yields were higher where SH was used than in plots with AS. The recovery of N by the first two consecutive harvests accounted for 19 to 21% of the N applied as leguminous green manure and 46 to 49% of the N applied as AS. The amounts of inorganic N, derived from both N sources, present in the 0-0.4 m layer of soil in the first season after N application and were below 1 kg ha-1. (author)

  19. Determination of nitrogenase activity of induced cucumber nodules by 15N Trace method

    The author reports the determination results of nitrogenase activity of induced cucumber root nodules by 15N trace method. The root systems bearing induced nodules of cucumber were exposed to a gas mixture containing 15N2 for 48 h and partial root systems soaked in free-nitrogen culture solution simultaneously. After exposure the 15N content in the modulated root systems of cucumber is 0.431 Atom % 15N by mass spectrometric analysis, whereas in the contrast samples without exposure to 15N is 0.369 Atom % 15N. The statistical t test for the results of 15N trace experiments is: t = 3.15 > t0.01 = 2.819. It has been demonstrated that the nitrogenase activity in cucumber nodules is at a remarkable level of 99.9%. The nitrogenase activity in detached nodules of cucumber was also determined by conventional acetylene reduction method. In both methods clear evidences of nitrogenase activity were obtained for the induced nodules of cucumber

  20. A sampling approach for protein backbone fragment conformations.

    Yu, J Y; Zhang, W

    2013-01-01

    In protein structure prediction, backbone fragment bias information can narrow down the conformational space of the whole polypeptide chain significantly. Unlike existing methods that use fragments as building blocks, the paper presents a probabilistic sampling approach for protein backbone torsion angles by modelling angular correlation of (phi, psi) with a directional statistics distribution. Given a protein sequence and secondary structure information, this method samples backbone fragments conformations by using a backtrack sampling algorithm for the hidden Markov model with multiple inputs and a single output. The proposed approach is applied to a fragment library, and some well-known structural motifs are sampled very well on the optimal path. Computational results show that the method can help to obtain native-like backbone fragments conformations. PMID:23777175

  1. LOAD AWARE ADAPTIVE BACKBONE SYNTHESIS IN WIRELESS MESH NETWORKS

    Yuan Yuan; Zheng Baoyu

    2009-01-01

    Wireless Mesh Networks (WMNs) are envisioned to support the wired backbone with a wireless Backbone Networks (BNet) for providing internet connectivity to large-scale areas.With a wide range of internet-oriented applications with different Quality of Service (QoS) requirement,the large-scale WMNs should have good scalability and large bandwidth.In this paper,a Load Aware Adaptive Backbone Synthesis (LAABS) algorithm is proposed to automatically balance the traffic flow in the WMNs.The BNet will dynamically split into smaller size or merge into bigger one according to statistic load information of Backbone Nodes (BNs).Simulation results show LAABS generates moderate BNet size and converges quickly,thus providing scalable and stable BNet to facilitate traffic flow.

  2. Alkaline Hydrolysis/Polymerization of 2,4,6-Trinitrotoluene: Characterization of Products by 13C and 15N NMR

    Thorn, K.A.; Thorne, P.G.; Cox, L.G.

    2004-01-01

    Alkaline hydrolysis has been investigated as a nonbiological procedure for the destruction of 2,4,6-trinitrotoluene (TNT) in explosives contaminated soils and munitions scrap. Nucleophilic substitutions of the nitro and methyl groups of TNT by hydroxide ion are the initial steps in the alkaline degradation of TNT. Potential applications of the technique include both in situ surface liming and ex situ alkaline treatment of contaminated soils. A number of laboratory studies have reported the formation of an uncharacterized polymeric material upon prolonged treatment of TNT in base. As part of an overall assessment of alkaline hydrolysis as a remediation technique, and to gain a better understanding of the chemical reactions underlying the hydrolysis/polymerization process, the soluble and precipitate fractions of polymeric material produced from the calcium hydroxide hydrolysis of unlabeled and 15N-labeled TNT were analyzed by elemental analysis and 13C and 15N nuclear magnetic resonance spectroscopy. Spectra indicated that reactions leading to polymerization included nucleophilic displacement of nitro groups by hydroxide ion, formation of ketone, carboxyl, alcohol, ether, and other aliphatic carbons, conversion of methyl groups to diphenyl methylene carbons, and recondensation of aromatic amines and reduced forms of nitrite, including ammonia and possibly hydroxylamine, into the polymer. Compared to the distribution of carbons in TNT as 14% sp 3- and 86% sp2-hybridized, the precipitate fraction from hydrolysis of unlabeled TNT contained 33% sp3- and 67% sp 2-hybridized carbons. The concentration of nitrogen in the precipitate was 64% of that in TNT. The 15N NMR spectra showed that, in addition to residual nitro groups, forms of nitrogen present in the filtrate and precipitate fractions include aminohydroquinone, primary amide, indole, imine, and azoxy, among others. Unreacted nitrite was recovered in the filtrate fraction. The toxicities and susceptibilities to

  3. Light-mediated 15N fractionation in Caribbean gorgonian octocorals: implications for pollution monitoring

    Baker, D. M.; Kim, K.; Andras, J. P.; Sparks, J. P.

    2011-09-01

    The stable nitrogen isotope ratio ( δ 15N) of coral tissue is a useful recorder of anthropogenic pollution in tropical marine ecosystems. However, little is known of the natural environmentally induced fractionations that affect our interpretation of coral δ 15N values. In symbiotic scleractinians, light affects metabolic fractionation of N during photosynthesis, which may confound the identification of N pollution between sites of varied depth or turbidity. Given the superiority of octocorals for δ 15N studies, our goal was to quantify the effect of light on gorgonian δ 15N in the context of monitoring N pollution sources. Using field collections, we show that δ 15N declined by 1.4‰ over 20 m depth in two species of gorgonians, the common sea fan, Gorgonia ventalina, and the slimy sea plume, Pseudopterogorgia americana. An 8-week laboratory experiment with P. americana showed that light, not temperature causes this variation, whereby the lowest fractionation of the N source was observed in the highest light treatment. Finally, we used a yearlong reciprocal depth transplant experiment to quantify the time frame over which δ 15N changes in G. ventalina as a function of light regime . Over the year, δ 15N was unchanged and increased slightly in the deep control colonies and shallow colonies transplanted to the deep site, respectively. Within 6 months, colonies transplanted from deep to shallow became enriched by 0.8‰, mirroring the enrichment observed in the shallow controls, which was likely due to the combined effect of an increase in the source δ 15N and reduced fractionation. We conclude that light affects gorgonian δ 15N fractionation and should be considered in sampling designs for N pollution monitoring. However, these fractionations are small relative to differences observed between natural and anthropogenic N sources.

  4. Utilization of 15N-Diammonium Phosphate by Ruminants to Produce Milk and Meat Proteins

    The authors investigated the alimentary role of diammonium phosphate (DAP) in ruminants. For this study DAP labelled with 15N was used; analysis of the 15N atomic per cent excess was made with an Italelettronica mass spectrophotometer (model SP 21 F) and the amino acid determination by a Beckman-Spinco amino acid analyser (model 120B) fitted with a preparative column. For the experiment 7 g of DAP at 15 and 20 at. % excess 15N were administered once to mature lactating and non-lactating sheep, respectively. The measurement of 15N in the protein and isolated amino acids of milk and meat showed: (1) The milk protein produced in the first 24 h contained the highest atomic per cent excess of 15SN, 0.093; (2) That the supplemental 15N was found in all the amino acids of milk proteins except tryptophane. The atomic per cent excess of 15N was observed to vary between the various amino acids. These results confirmed previous observations on bacterial protein synthesized from DAP. (3) Muscle protein 15N maximized on the third day after administration of the 15N-DAP, with an atomic per cent excess of 0.040; (4) The atomic per cent excess of 15N in the individual amino acids of muscle protein is significant in only two amino' acids, serine and cystine; and (5) That after 8 d of adaptation there are no traces of DAP in milk or meat proteins, urine or faeces. The authors conclude that the ruminant, after a period of adaptation and through the mediation of ruminant microorganisms, is able to use the nitrogen of diammonium phosphate for the synthesis of milk and meat proteins. (author)

  5. Absorption and metabolization of orally administered D-[α-15N]lysine and L-[α-15N]lysine with regard to the metabolism of intestinal bacteria

    Absorption of D-[α-15N]lysine and L-[α-15N]lysine following oral single pulse-labelling at a dosage of 5 mg 15N'/kg body weight was compared in four subjects aged 4 to 14 months. The wastages of 15N' in the feces ranged from 0.3 to 5% of the input implying comparably high absorption rates of both the lysine enantiomers. Only about 7.6% of the 15N from the α-amino groups were found in the urine after loading with L-[α-15N]lysine. In contrast, about 80.2% of the 15N' dose from D-[α-15N]lysine were eliminated renally. However, 18.5% of the 15N' dose on an average were retained after D-[α-15N]lysine administration. This is certainly due to a partial desamination of D-lysine. The fecal bacteria isolated from the feces contained no or only small amounts of 15N' after D-[α-15N]lysine loading. Following L-[α-15N]lysine administration a measurable 15N enrichment of the fecal bacteria of up to 0.09 at.% excess was achieved in almost all cases. (author)

  6. Sequence-specific {sup 1}H, {sup 13}C, and {sup 15}N resonance assignments for intestinal fatty-acid-binding protein complexed with palmitate (15.4 kDA)

    Hodsdon, M.E.; Toner, J.J.; Cistola, D.P. [Washington Univ. School of Medicine, St. Louis, MO (United States)

    1994-12-01

    Intestinal fatty-acid-binding protein (I-FABP) belongs to a family of soluble, cytoplasmic proteins that are thought to function in the intracellular transport and trafficking of polar lipids. Individual members of this protein family have distinct specificities and affinities for fatty acids, cholesterol, bile salts, and retinoids. We are comparing several retinol- and fatty-acid-binding proteins from intestine in order to define the factors that control molecular recognition in this family of proteins. We have established sequential resonance assignments for uniformly {sup 13}C/{sup 15}N-enriched I-FABP complexed with perdeuterated palmitate at pH7.2 and 37{degrees}C. The assignment strategy was similar to that introduced for calmodulin. We employed seven three-dimensional NMR experiments to establish scalar couplings between backbone and sidechain atoms. Backbone atoms were correlated using triple-resonance HNCO, HNCA, TOCSY-HMQC, HCACO, and HCA(CO)N experiments. Sidechain atoms were correlated using CC-TOCSY, HCCH-TOCSY, and TOCSY-HMQC. The correlations of peaks between three-dimensional spectra were established in a computer-assisted manner using NMR COMPASS (Molecular Simulations, Inc.) Using this approach, {sup 1}H, {sup 13}C, and {sup 15}N resonance assignments have been established for 120 of the 131 residues of I-FABP. For 18 residues, amide {sup 1}H and {sup 15}N resonances were unobservable, apparently because of the rapid exchange of amide protons with bulk water at pH 7.2. The missing amide protons correspond to distinct amino acid patterns in the protein sequence, which will be discussed. During the assignment process, several sources of ambiguity in spin correlations were observed. To overcome this ambiguity, the additional inter-residue correlations often observed in the HNCA experiment were used as cross-checks for the sequential backbone assignments.

  7. 使用Backbone JS搭建SPA

    吕婷

    2012-01-01

    Backbone JSR从2010年发布以来,受到了业界的广泛关注。“豆瓣说”和“豆瓣阅读(阅读器)”是两款以它为基础框架搭建的SPA,本文将结合这两款产品,向读者介绍BackboneJS的方方面面。

  8. Side chain and backbone ordering in a polypeptide

    Wei, Y; Hansmann, U H E

    2006-01-01

    We report results from multicanonical simulations of polyglutamic acid chains of length of ten residues. For this simple polypeptide we observe a decoupling of backbone and side-chain ordering in the folding process. While the details of the two transitions vary between the peptide in gas phase and in an implicit solvent, our results indicate that, independent of the specific surroundings, upon continuously lowering the temperature side-chain ordering occurs only after the backbone topology is completely formed.

  9. Radiative p 15N Capture in the Region of Astrophysical Energies

    Dubovichenko, S. B.; Burtebaev, N.; Dzhazairov-Kakhramanov, A. V.; Alimov, D. K.

    2016-06-01

    Within the framework of the modified potential cluster model with classification of orbital states according to the Young schemes, the possibility of describing experimental data for the astrophysical S-factor of p 15N radiative capture at energies from 50 to 1500 keV is considered. It is shown that on the basis of M1 and E1 transitions from various p 15N scattering states to the ground state of the 16O nucleus in the p 15N channel it is entirely possible to successfully explain the overall behavior of the S-factor in the considered energy region in the presence of two resonances.

  10. Nitrogen distribution a 15 N fertilizer in different soil fractions of a barley cultivation

    A culture of barley in the open fields has been fertilized on 9 m2 with Ca(NO3)2 containing 20,8% 15N excess. At the crop, 15 N distribution shows that half of the fertilized nitrogen which is exported by the crop has become organic in the Ap horizon. The use of different methods of fractionation of the soil, shows the biological character of this reorganization, in which the biomass appears to be the main 15 N nitrogen stock

  11. Large-scale measurement and modeling of backbone Internet traffic

    Roughan, Matthew; Gottlieb, Joel

    2002-07-01

    There is a brewing controversy in the traffic modeling community concerning how to model backbone traffic. The fundamental work on self-similarity in data traffic appears to be contradicted by recent findings that suggest that backbone traffic is smooth. The traffic analysis work to date has focused on high-quality but limited-scope packet trace measurements; this limits its applicability to high-speed backbone traffic. This paper uses more than one year's worth of SNMP traffic data covering an entire Tier 1 ISP backbone to address the question of how backbone network traffic should be modeled. Although the limitations of SNMP measurements do not permit us to comment on the fine timescale behavior of the traffic, careful analysis of the data suggests that irrespective of the variation at fine timescales, we can construct a simple traffic model that captures key features of the observed traffic. Furthermore, the model's parameters are measurable using existing network infrastructure, making this model practical in a present-day operational network. In addition to its practicality, the model verifies basic statistical multiplexing results, and thus sheds deep insight into how smooth backbone traffic really is.

  12. 13C and 15N fractionation of CH4/N2 mixtures during photochemical aerosol formation: Relevance to Titan

    Sebree, Joshua A.; Stern, Jennifer C.; Mandt, Kathleen E.; Domagal-Goldman, Shawn D.; Trainer, Melissa G.

    2016-05-01

    The ratios of the stable isotopes that comprise each chemical species in Titan's atmosphere provide critical information towards understanding the processes taking place within its modern and ancient atmosphere. Several stable isotope pairs, including 12C/13C and 14N/15N, have been measured in situ or probed spectroscopically by Cassini-borne instruments, space telescopes, or through ground-based observations. Current attempts to model the observed isotope ratios incorporate fractionation resulting from atmospheric diffusion, hydrodynamic escape, and primary photochemical processes. However, the effect of a potentially critical pathway for isotopic fractionation - organic aerosol formation and subsequent deposition onto the surface of Titan - has not been considered due to insufficient data regarding fractionation during aerosol formation. To better understand the nature of this process, we have conducted a laboratory study to measure the isotopic fractionation associated with the formation of Titan aerosol analogs, commonly referred to as 'tholins', via far-UV irradiation of several methane (CH4) and dinitrogen (N2) mixtures. Analysis of the δ13C and δ15N isotopic signatures of the photochemical aerosol products using an isotope ratio mass spectrometer (IRMS) show that fractionation direction and magnitude are dependent on the initial bulk composition of the gas mixture. In general, the aerosols showed enrichment in 13C and 14N, and the observed fractionation trends can provide insight into the chemical mechanisms controlling photochemical aerosol formation.

  13. Near-complete (1)H, (13)C, (15)N resonance assignments of dimethylsulfoxide-denatured TGFBIp FAS1-4 A546T.

    Kulminskaya, Natalia V; Yoshimura, Yuichi; Runager, Kasper; Sørensen, Charlotte S; Bjerring, Morten; Andreasen, Maria; Otzen, Daniel E; Enghild, Jan J; Nielsen, Niels Chr; Mulder, Frans A A

    2016-04-01

    The transforming growth factor beta induced protein (TGFBIp) is a major protein component of the human cornea. Mutations occurring in TGFBIp may cause corneal dystrophies, which ultimately lead to loss of vision. The majority of the disease-causing mutations are located in the C-terminal domain of TGFBIp, referred as the fourth fascilin-1 (FAS1-4) domain. In the present study the FAS1-4 Ala546Thr, a mutation that causes lattice corneal dystrophy, was investigated in dimethylsulfoxide using liquid-state NMR spectroscopy, to enable H/D exchange strategies for identification of the core formed in mature fibrils. Isotope-labeled fibrillated FAS1-4 A546T was dissolved in a ternary mixture 95/4/1 v/v/v% dimethylsulfoxide/water/trifluoroacetic acid, to obtain and assign a reference 2D (1)H-(15)N HSQC spectrum for the H/D exchange analysis. Here, we report the near-complete assignments of backbone and aliphatic side chain (1)H, (13)C and (15)N resonances for unfolded FAS1-4 A546T at 25 °C. PMID:26275916

  14. Measurement of marine productivity using 15N and 13C tracers: Some methodological aspects

    Naveen Gandhi; Sanjeev Kumar; S Prakash; R Ramesh; M S Sheshshayee

    2011-02-01

    Various experiments involving the measurement of new, regenerated and total productivity using 15N and 13C tracers were carried out in the Bay of Bengal (BOB) and in the Arabian Sea. Results from 15N tracer experiments indicate that nitrate uptake can be underestimated by experiments with incubation time > 4 hours. Indirect evidence suggests pico- and nano-phytoplankton, on their dominance over microphytoplankton, can also influence the f-ratios. Difference in energy requirement for assimilation of different nitrogen compounds decides the preferred nitrogen source during the early hours of incubation. Variation in light intensity during incubation also plays a significant role in the assimilation of nitrogen. Results from time course experiments with both 15N and 13C tracers suggest that photoinhibition appears significant in BOB and the Arabian Sea during noon. A significant correlation has been found in the productivity values obtained using 15N and 13C tracers.

  15. Direct measurement of the {sup 15}N CSA/dipolar relaxation interference from coupled HSQC spectra

    Hall, Jennifer B. [University of Maryland, Department of Chemistry and Biochemistry, Center of Biomolecular Structure and Organization (United States); Dayie, Kwaku T. [Lerner Research Institute, Cleveland Clinic Foundation, Department of Molecular Biology, Center for Structural Biology (United States); Fushman, David [University of Maryland, Department of Chemistry and Biochemistry, Center of Biomolecular Structure and Organization (United States)], E-mail: fushman@wam.umd.edu

    2003-06-15

    Here we propose a method for the measurement of the {sup 15}N CSA/dipolar relaxation interference based on direct comparison of the {sup 15}N doublet components observed in a {sup 1}H-coupled {sup 1}H-{sup 15}N HSQC-type spectrum. This allows the determination of the cross-correlation rates with no need for correction factors associated with other methods. The signal overlap problem of coupled HSQC spectra is addressed here by using the IPAP scheme (Ottiger et al., 1998). The approach is applied to the B3 domain of protein G to show that the method provides accurate measurements of the {sup 15}N CSA/dipolar cross-correlation rates.

  16. Evaluation of the protein metabolism during hepatic coma evidenced by 15N tracer data

    In patients in coma hepaticum as well as in pigs with experimental hepatic coma the protein metabolism was studied under conditions of parenteral application of an amino acid diet using 15N-glycine as tracer

  17. 14N and 15N imaging by SIMS microscopy in soybean leaves

    The distribution of 15N and 14N compounds in cryofixed and resin embedded sections of soybean (Glycine max L) leaves was studied by SIMS microscopy. The results indicate that, with a mass resolution M/ΔM higher than 6000, images of the nitrogen distribution can be obtained from the mapping of the two secondary cluster ions 12C14N− and 12C15N−, in samples of both control and 15N-labeled leaves. The ionic images were clearly related to the histological structure of the organ, and allow the detection of 14N and 15N at the subcellular level. Furthermore, relative measurements of the 12C14N− and 12C15N− beams made possible the quantification of the 15N atom% in the various tissues of the leaf. (author)

  18. Metabolic studies in colostomized laying hens using 15N-labelled wheat. 3

    In colostomized laying hens fed with 15N-labelled wheat protein the atomic percentage 15N excess (15N') was determined in the total, lysine, histidine, and arginine N, respectively, of isolated ovarian follicles of the residual ovary and of the oviduct. The labelling of the basic amino acids became smaller with decreasing size of the follicles. The proportions between the 3 amino acids were inconsistent and typical for the individual hens, whereas in the yolk a constant ratio of the amino acids was found. The 15N' in the 3 amino acids of the residual ovary and of the oviduct revealed greater differences between the individual hens. In the lysine, histidine and arginine 21.2% of the labelled N of the follicles was demonstrated

  19. Synthesis of nitric oxide releasing, vasodilating and platelet aggregation inhibiting S-[15N]nitroso compounds

    [15N]Nitric oxide (15NO) was produced in a ''gastight'' flask from [15N]nitrite by reaction with iodide in acetic acid acidified water and purged for 60 min by a continuous nitrogen gas stream applied through an uncoated polytetrafluoroethylene flate membrane into a second flask which contained a methanolic solution of N-acetyl-L-cysteine or N-acetyl-DL-penicillamine. Analysis of these solutions by UV spectroscopy, reversed-phase high-performance liquid chromatography and capillary isotachophoresis showed formation of the corresponding S-nitroso compounds. Gas chromatographic-mass spectrometric analysis for [15N]nitrite which was formed by dissolving these compounds in aqueous buffered solutions gave an isotopic purity higher than 95% at 15N. The S-nitroso compounds were shown to inhibit ADP-induced platelet aggregation. (author)

  20. Methodical investigation of the endogenous N excretion in feces by 15N-labelled rats

    Wistar rats (approximately 100g live weight, n = 8) received a wheat diet and were labelled over a period of 7 days with 15N-ammonium acetate. From day 1 - 5 of the experiment after the end of the labelling feces and urine were collected and analysed. After the animals were killed (day 5 of the experiment) the atom-% 15N excess (15N') in the contents of the digestive tract as well as in the tissues of stomach wall, intestinal wall, liver, pancreas and blood plasma was determined. The TCA-soluble fraction of the blood plasma showed 0.44 atom-% 15N' on day 5 after the end of 15N labelling. 3 hours before the killing fecal N also showed 0.44 and during the last collection period (24 hours before) an average of 0.51 atom-% 15N'. Urine decreased in the same period from 0.71 to 0.59 atom-% 15N'. The endogenous fecal N is calculated to 88%. As the tissues of the digestive tract are likely to supply the biggest part of the endogenous fecal protein, the values of atom-% 15N' from the TCA-precipitable fraction of the intestinal wall and of the pancreas gland was calculed to an average of 0.526. According to this the calculation endogenous fecal N is 84%. It is probable that the quota of endogenous fecal N in the total amount of fecal N varies in dependence on the fermentable crude fiber in the diet as well as on the age of the test animals and thus the bacterial protein synthesis in the colon. As the N used by the bacteria is likely to come from the TCA-soluble fraction of the blood, the calculation formula suggested, which uses the TCA-soluble fraction of the blood plasma, achieves good approximate values also for higher bacterial protein synthesis in the colon. (author)

  1. λ cro repressor complex with O/sub R/3 DNA: 15N NMR observations

    15N NMR studies of the coliphage λ cro repressor are presented. The protein has been uniformly labeled with 15N, and individual amino acids have been incorporated. Although the four C-terminal residues (63-66) were not located in the original crystallographic studies of the protein it has been proposed that the C-terminus is involved in DNA binding. These experiments give direct verification of that proposal. [15N] Amide resonances are assigned for residues 56, 62, 63, and 66 in the C-terminus by enzymatic digestion and by 13C-15N double-labeling experiments. 15N{1H} nuclear Overhauser effects show that the C-terminus is mobile on a nanosecond time scale. Exchange experiments using distortionless enhancement via polarization transfer, which is sensitive to proton exchange on the 1/J/sub NH/(10 ms) time scale, indicate that the amide protons in the C-terminus are freely accessible to solvent. It is thus a flexible arm in solution. The binding of both specific operator and nonspecific DNA is shown to reduce both the mobility and the degree of solvent exposure of this arm. Two-dimensional 15N-1H correlation experiments using 15N-labeled cro reveal inconsistencies with previously reported 1H NMR assignments for the lysine amides. This result suggests that those assignments require reexamination, illustrating the utility of 15N labeling for obtaining 1H resonance assignments of biomolecules. Furthermore, isomerization of the peptide bond of Pro-59, which has been previously suggested and which would significantly affect the properties of the C-terminal arm, is shown to not occur

  2. Temperature {sup 1}H, {sup 13}C, {sup 15}N NMR and CP/MAS {sup 15}N NMR spectra of benzotriazole derivatives - prototropic tautomerism; Widma temperaturowe {sup 1}H, {sup 13}C, {sup 15}N NMR oraz CP/MAS {sup 15}N NMR pochodnych benzotriazolu - tautomeria prototropowa

    Wiench, J.W.; Stefaniak, L. [Inst. Chemii Organicznej, Polska Akademia Nauk, Warsaw (Poland)

    1994-12-31

    The prototropic tautomerism in benzotriazole derivatives solutions has been investigated in different temperatures by means of {sup 1}H, {sup 13}C and {sup 15}N NMR and {sup 15}N CP/MAS NMR spectra. The ratio of different tautomeric forms and kinetics of proton exchange have been measured for the systems studied on the base of observed spectroscopic factors. 5 refs, 2 figs, 3 tabs.

  3. 15N abundance in Antarctica: origin of soil nitrogen and ecological implications

    The results of an investigation of the nitrogen cycle in Antartica are reported which show that nitrate in Antarctic soils is extremely depleted in 15N compared with biogenic nitrogen and that algae collected from a nitrate-rich saline pond and from a penguin rookery exhibit, respectively, the lowest and the highest 15N/14N ratios among terrestrial biogenic nitrogen so far observed. The possible causes of these extreme nitrogen isotopic compositions are discussed. (U.K.)

  4. Denitrification by intact soybean nodules in relation to natural 15N enrichment of nodules

    The natural 15N abundance of nodules of soybeans (Glycine max (L.) Merrill) which are actively fixing N2 is considerably higher than other tissues. To investigate the question of whether isotopic fractionation associated with denitrification by bacteroids causes this 15N enrichment, we inoculated soybeans with two strains of Rhizobium japonicum. Free-living cultures of one of these (strain USDA 33) were unable to denitrify or respire NO3-, while free-living cultures of the second (strain USDA 138) were capable of denitrification. USDA 138 formed nodules which fixed N2 very efficiently. The N of these nodules was enriched in 15N and the nodules reduced a substantial amount of NO3- to NO2- and N2O. Nodules infected with USDA 33 fixed about half as much N2 as those infected with USDA 138. The former nodules were enriched in 15N (although less so than nodules infected with USDA 138), despite the fact that the nodules formed by USDA 33 did not reduce NO3-. Clearly denitrification could not have been the cause of 15N enrichment of nodules infected with strain USDA 33. Alternative causes of 15N enrichment of soybean nodules and their possible metabolic significance are discussed

  5. Use of 15N to measure nitrogen uptake in eutrophic oceans; experimental considerations

    The use of 15N to measure the flux of nitrogen compounds has become increasingly popular as the techniques and instrumentation for stable isotope analysis have become more widely available. Questions concerning equations for calculating uptake, effect of isotope dilution (in the case of ammonium), duration of incubation, and relationship between disappearance of a nitrogen compound and the 15N uptake measurement have arisen, especially for the research conducted in oligotrophic regions. Fewer problems seem to have occurred ineutrophic areas. However, sufficient literature now exists to allow some generally accepted experimental procedures for 15N studies in eutrophic regions to be laid down. Incubation periods of 2-6 h appear to avoid problems related to isotope dilution and to overcome the bias introduced in some cases by initial high rate or surge uptake. During such incubation periods, assimilation is measured rather than uptake or transport into the cell. Incorporation of 15N into the particulate fraction is usually linear with time over the periods currently used. The 15N method provides a better estimate of incorporation into phytoplankton than 14N disappearance, but a small fraction appears to be lost. Although most workers suggest the loss to be a result of dissolved organic nitrogen production, direct evidence is lacking. If the considerations discussed here are applied with the 15N techniques currently available, reliable estimates of phytoplankton nitrogen flux in eutrophic areas can be obtained

  6. Synthesis of methotrexate-1-15N and methotrexate-4-15NH2

    This paper describes an application of the pterin synthesis of methotrexate specifically labelled at the N1-ring nitrogen and at the 4-amino group with 99 atom percent 15N. Oximination of ethyl cyanoacetate-15N followed by reduction afforded ethyl 2-aminocyanoacetate-C15N. Condensation with 3-bromopyruvaldoxime and 4-methylamino-benzoic acid afforded 2-amino-3-carbethoxy-5-N-methyl-p-carboxy-anilinomethylpyrazine-1-oxide-2-15NH2. Treatment with ammonium hydroxide at room temperature gave the 3-carboxamide. Reduction of the N-oxide (Pl3), esterification, and dehydration of the amide (POCl3) afforded the 2-amino-3-cyano-pyrazine benzoate ester. Ring closure with guanidine followed by benzoate ester hydrolysis, glutamate coupling and hydrolysis of the glutamate diester yielded methotrexate-1-15N. Animation of the unlabeled 2-amino-3-carbethoxy pyrazine intermediate with 15N-labelled ammonium hydroxide gave the 15N-carboxamide which was carried through the process described above to afford methotrexate-4-15NH2. (author)

  7. Metabolism of [15N]alanine in the ectomycorrhizal fungus Paxillus involutus

    Chalot, M., Finlay, R. D., Ek, H., and Söderström, B. 1995. Metabolism of [15N]alanine in the ectomycorrhizal fungus Paxillus involutus. Experimental Mycology 19, 297-304. Alanine metabolism in the ectomycorrhizal fungus Paxillus involutus was investigated using [15N]alanine. Short-term exposure of mycelial discs to [15N]alanine showed that the greatest flow of 15N was to glutamate and to aspartate. Levels of enrichment were as high as 15-20% for glutamate and 13-18% for aspartate, whereas that of alanine reached 30%. Label was also detected in the amino-N of glutamine and in serine and glycine, although at lower levels. Preincubation of mycelia with aminooxyacetate, an inhibitor of transamination reactions. resulted in complete inhibition of the flow of the label to glutamate, aspartate, and amino-N of glutamine, whereas [15N]alanine rapidly accumulated. This evidence indicates the direct involvement of alanine aminotransferase for translocation of 15N from alanine to glutamate. Alanine may be a convenient reservoir of both nitrogen and carbon. (author)

  8. Quantifying below-ground nitrogen of legumes: Optimizing procedures for 15N shoot-labelling

    Quantifying below-ground nitrogen (N) of legumes is fundamental to understanding their effects on soil mineral N fertility and on the N economies of following or companion crops in legume-based rotations. Methodologies based on 15N-labelling of whole plants with subsequent measurement of 15N in recovered plant parts and in the root-zone soil have proved promising. We report four glasshouse experiments with objectives to develop appropriate protocols for in situ 15N labelling of four pulses, faba bean (Vicia faba), chickpea (Cicer arietinum), mung bean (Vigna radiata) and pigeon pea (Cajanus cajan). Treatments included 15N-urea concentration, feeding technique, leaflet/petiole position, and frequency of feeding. Nitrogen-15-labelling via the leaf-flap was best for faba bean, mung and pigeon pea, whilst petiole feeding was best for chickpea, in all cases using 0.2-mL volumes of 0.5% urea (98 atom% 15N excess). The implications of uneven enrichment of the nodulated roots because of effects of the 15N-depleted nodules when calculating root-derived N in soil are discussed. (author)

  9. Nitrogen dynamics in a Western Boundary Upwelling System (Cabo Frio, Brazil) based on δ15N-nitrate and δ15N of sinking particle signals

    Fontana, L.; Belem, A. L.; Venancio, I.; Duarte, C.; Chiara, S. D.; Albuquerque, A. L.

    2014-12-01

    To improve the efficiency of upwelling to control nitrogen dynamic in the ocean, better understanding of the occurring processes is necessary. This research explores δ15N of nitrate and sinking particles on a western boundary upwelling System (Cabo Frio, Brazil). The Continental Shelf of southeastern Brazil is dominated by the oligotrophic Brazil Current, whose instabilities promote the coastal upwelling of South Atlantic Central Water (SACW), and consequently increases of primary productivity. The coastal upwelling system plays an important role in the nitrogen dynamics on the Cabo Frio Upwelling System (CFUS). However, the interactions between biological induced processes, including biological N-fixation and nitrate inputs from upwelled waters in CFUS still have not been well explored. Then, this study aims clarify N-dynamics on CFUS based on a cross-shelf approach. δ15N-nitrate was characterized for each water masses present on the shelf (South Atlantic Central Water, Tropical Water and Coastal Water) and associated with physicochemical parameters (T/S, nutrients), as well as the δ15N of sinking particles at different depths (from surface to the bottom water). Samples were collected in a time interval of 1 month during ~4 years (2011 to 2014). Cross-shelf gradients of nitrogen species concentration (ammonium + nitrite + nitrate) and stable isotopes were observed. The δ15N of nitrate and sinking particles were interpreted according to the prevailing processes of the N-transformations. Considering the region as N-limited (N:P global average of deep ocean (5-6‰) characterizing the inner and mid-shelf conditions, where the input of new nitrate from upwelling is rapidly used by organisms in the euphotic zone without any fractionation. On the other hands, the dominance of N-limited Tropical Waters on the outer shelf provide a δ15N-nitrate and δ15N-sinking particles signals (-2.0 to 3.0‰) lower than the global average of deep ocean range indicating the

  10. Revision of the 15N(p, γ)16O reaction rate and oxygen abundance in H-burning zones

    Caciolli, A.; Mazzocchi, C.; Capogrosso, V.; Bemmerer, D.; Broggini, C.; Corvisiero, P.; Costantini, H.; Elekes, Z.; Formicola, A.; Fülöp, Zs.; Gervino, G.; Guglielmetti, A.; Gustavino, C.; Gyürky, Gy.; Imbriani, G.; Junker, M.; Lemut, A.; Marta, M.; Menegazzo, R.; Palmerini, S.; Prati, P.; Roca, V.; Rolfs, C.; Rossi Alvarez, C.; Somorjai, E.; Straniero, O.; Strieder, F.; Terrasi, F.; Trautvetter, H. P.; Vomiero, A.

    2011-09-01

    Context. The NO cycle takes place in the deepest layer of a H-burning core or shell, when the temperature exceeds T ≃ 30 × 106 K. The O depletion observed in some globular cluster giant stars, always associated with a Na enhancement, may be due to either a deep mixing during the red giant branch (RGB) phase of the star or to the pollution of the primordial gas by an early population of massive asymptotic giant branch (AGB) stars, whose chemical composition was modified by the hot bottom burning. In both cases, the NO cycle is responsible for the O depletion. Aims: The activation of this cycle depends on the rate of the 15N(p, γ)16O reaction. A precise evaluation of this reaction rate at temperatures as low as experienced in H-burning zones in stellar interiors is mandatory to understand the observed O abundances. Methods: We present a new measurement of the 15N(p, γ)16O reaction performed at LUNA covering for the first time the center of mass energy range 70-370 keV, which corresponds to stellar temperatures between 65 × 106 K and 780 × 106 K. This range includes the 15N(p, γ)16O Gamow-peak energy of explosive H-burning taking place in the external layer of a nova and the one of the hot bottom burning (HBB) nucleosynthesis occurring in massive AGB stars. Results: With the present data, we are also able to confirm the result of the previous R-matrix extrapolation. In particular, in the temperature range of astrophysical interest, the new rate is about a factor of 2 smaller than reported in the widely adopted compilation of reaction rates (NACRE or CF88) and the uncertainty is now reduced down to the 10% level.

  11. Automated assignment of NMR chemical shifts based on a known structure and 4D spectra.

    Trautwein, Matthias; Fredriksson, Kai; Möller, Heiko M; Exner, Thomas E

    2016-08-01

    Apart from their central role during 3D structure determination of proteins the backbone chemical shift assignment is the basis for a number of applications, like chemical shift perturbation mapping and studies on the dynamics of proteins. This assignment is not a trivial task even if a 3D protein structure is known and needs almost as much effort as the assignment for structure prediction if performed manually. We present here a new algorithm based solely on 4D [(1)H,(15)N]-HSQC-NOESY-[(1)H,(15)N]-HSQC spectra which is able to assign a large percentage of chemical shifts (73-82 %) unambiguously, demonstrated with proteins up to a size of 250 residues. For the remaining residues, a small number of possible assignments is filtered out. This is done by comparing distances in the 3D structure to restraints obtained from the peak volumes in the 4D spectrum. Using dead-end elimination, assignments are removed in which at least one of the restraints is violated. Including additional information from chemical shift predictions, a complete unambiguous assignment was obtained for Ubiquitin and 95 % of the residues were correctly assigned in the 251 residue-long N-terminal domain of enzyme I. The program including source code is available at https://github.com/thomasexner/4Dassign . PMID:27484442

  12. Backbone Fragility and the Local Search Cost Peak

    Gent, I P; Smaill, A; 10.1613/jair.711

    2011-01-01

    The local search algorithm WSat is one of the most successful algorithms for solving the satisfiability (SAT) problem. It is notably effective at solving hard Random 3-SAT instances near the so-called `satisfiability threshold', but still shows a peak in search cost near the threshold and large variations in cost over different instances. We make a number of significant contributions to the analysis of WSat on high-cost random instances, using the recently-introduced concept of the backbone of a SAT instance. The backbone is the set of literals which are entailed by an instance. We find that the number of solutions predicts the cost well for small-backbone instances but is much less relevant for the large-backbone instances which appear near the threshold and dominate in the overconstrained region. We show a very strong correlation between search cost and the Hamming distance to the nearest solution early in WSat's search. This pattern leads us to introduce a measure of the backbone fragility of an instance, ...

  13. Acetylene inhibition of N2O reduction in laboratory soil and groundwater denitrification assays: evaluation by 15N tracer and 15N site preference of N2O

    Weymann, Daniel; Well, Reinhard; Lewicka-Szczebak, Dominika; Lena, Rohe

    2013-04-01

    The measurement of denitrification in soils and aquifers is still challenging and often enough associated with considerable experimental effort and high costs. Against this background, the acetylene inhibition technique (AIT) applied in laboratory soil and groundwater denitrification assays is by far the most effective approach. However, this method has been largely criticized, as it is susceptible to underestimate denitrification rates and adds an additional carbon source to the substrates to be investigated. Here we provide evidence that the AIT is not necessarily an inappropriate approach to measure denitrification, that its reliability depends on the drivers governing the process, and that the 15N site preference of N2O (SP) may serve as a tool to assess this reliability. Two laboratory batch experiments were conducted, where sandy aquifer material and a peat soil were incubated as slurries. We established (i) a standard anaerobic treatment by adding KNO3 (10 mg N L-1), (ii) an oxygen treatment by adding KNO3 and O2 (5 mg L-1), and (iii) a glucose treatment by adding KNO3 supplemented with glucose (200 mg C L-1). Both experiments were run under 10 % (v/v) acetylene atmosphere and as 15N tracer treatments using labeled K15NO3 (60 atom % 15N). In the case of the standard anaerobic treatments, we found a very good agreement of denitrification potential obtained by the AIT and 15N tracer methods. SP of N2O of the AIT samples from this treatment ranged between -4.8 and 2.6 ‰ which is indicative for N2O production during bacterial denitrification but not for N2O reduction to N2. In contrast, we observed substantial underestimation of denitrification by AIT for the glucose treatments compared to the 15N method, i.e. denitrification was underestimated by 36 % (sandy aquifer material) and 47 % (peat soil). SP of N2O of the AIT samples from this treatment ranged between 4.5 and 9.6 ‰, which suggests occurrence of bacterial N2O reduction. In the case of the oxygen

  14. Stickstoffausnutzungseffizienz von 15N-markierter Schafsgülle und 15N-markiertem Mineraldünger in biologisch und konventionell bewirtschafteten Anbausystemen

    Bosshard, Christine; Sorensen, Peter; Frossard, Emmanuel; Mayer, Jochen; Mäder, Paul; Nanzer, Simone; Oberson, Astrid

    2009-01-01

    Nitrogen (N) utilisation by crops has to be improved to minimize losses to the environment. We investigated N use efficiency of animal manure and mineral fertiliser and fate of fertiliser N not taken up by crops in a bio-organic (BIOORG) and a conventional (CONMIN) cropping system of a long-term experiment over three vegetation periods (wheat-soybean-maize). Microplots received a single application of 15N-labelled slurries or mineral fertiliser. At the end of each vegetation pe...

  15. evaluation of biological nitrogen fixation process by chickpea using 15N tracer techniques

    the effect of gradual increase in fertilizer-N rates added to chickpea plants that cultivated in pots packed with light textured soil collected from surrounding area of biotechnology research center, libya was examined in pot experiment. seeds were inoculated with rhizobium strain as peat-based inocula or in liquid culture. Also, un inoculated treatment was included. 15 N-labelled urea(5% atom excess) was applied as N-fertilizer source at rates of 0,20, 40,60,80 and 100 Kg N ha-1. growth parameters of chickpea plants were positively affected by N-fertilizer but bacterial inoculation did not reflected significant difference with levels of 40,60 and 80 kg ha-1..dry matter accumulation was increased with increasing N fertilizer levels up to 80 Kg N ha-1 as compared to the unfertilized control then decreased at the level of 100 kg N ha-1. this holds true under inoculated and un inoculated treatments. similar trend was noticed with nitrogen uptake by chickpea shoots.accordingly, portion of N derived from fertilizer had been increased. nitrogen fixation (% N dfa), as estimated using isotope dilution approach, was increased with increasing N rates up to moderate additions (60 kg N ha-1) , then tended to decrease. Rhizobium inoculation has an important effect on enhancement of plant growth and N acquisition when low to moderate levels of fertilizer was added. The results obtained in this work suggests application of bio fertilization technology in combination with chemical fertilizers under field conditions to get advanced to generalize the data released from such investigations

  16. Absorption of ammonium sulphate {sup 15}N by coffee plants; Recuperacao do {sup 15}N do sulfato de amonio por plantas de cafe

    Fenilli, Tatiele Anete Bergamo; Reichardt, Klaus; Bacchi, Osny Oliveira Santos [Centro de Energia Nuclear na Agricultura (CENA), Piracicaba, SP (Brazil). Lab. de Fisica do Solo]. E-mail: tatiele@cena.usp.br; Trivelin, Paulo Cesar Ocheuze [Centro de Energia Nuclear na Agricultura (CENA), Piracicaba, SP (Brazil). Lab. de Isotopos Estaveis; Dourado Neto, Durval [Sao Paulo Univ., Piracicaba, SP (Brazil). Escola Superior de Agricultura Luiz de Queiroz. Dept. de Producao Vegetal

    2005-07-01

    The objective of this study was to quantify the absorption of ammonium sulphate {sup 15}N by coffee plants. Treatments consisted of five sub-plots of 9 plants, of which the three central ones received 280 kg ha{sup -1} of {sup 15}N, applied at four times: 1/4 on 01 Set 03; 1/4 on 03 Nov 03; 1/4 on 15 Dec 03 and 1/4 on 30 Jan 04. The isotopic enrichment was 2,072 {+-} 0,001 atom % {sup 15}N. The dry matter of the shoot was evaluated every 60 days, using one plant per replicate, collected outside the sub-plot. They were as similar as possible to the labeled plants, which were used only for isotopic and Total N analysis, after being dried at 65 deg C until constant weight. At harvest, plants had absorbed 42,88% of the fertilizer N. Leaves accumulated the largest amount of fertilizer N, and were also the compartments that received most N from other parts of the plant. The following partition of the fertilizer N was found at harvest: 23.01% in young leaves, 6.23% in old leaves, 4,46% in stem, 3.46% in fruits, 3.10% in young branches and 2.63% in old branches. (author)

  17. Barley Benefits from Organic Nitrogen in Plant Residues Applied to Soil using 15N Isotope Dilution

    The experiment was carried out in pots (sandy soil cultivated with Barley plant) under greenhouse conditions, at Inshas, Egypt. The aim was to evaluate the transformation of nitrogen applied either as mineral form (15NH4)2SO4, or as organic-material-N (plant residues) .Basal recommended doses of P and K were applied. Labeled 15N as(15NH4)2SO4 (5 % a.e) or plant residues (ground leuceana forage, compost, and mixture of them) were applied at a rate of 20 kg N/ ha). 15N technique was used to evaluate N-uptake and fertilizer use efficiency. The treatments were arranged in a completely randomized block design under greenhouse conditions. The obtained results showed that the dry weight of barley shoots was positively affected by reinforcement of mineral- N with organic-N. On the other hand, the highest dry weight was estimated with leuceana either applied alone or reinforced with mineral N. Similar trend was noticed with N uptake but only with organic N, while with treatment received 50% organic-N. plus 50% mineral- N. the best value of N uptake was recorded with mixture of leuceana and compost. The amount of Ndff was lowest where fertilizer 15N was applied alone. Comparing Ndff for the three organic treatments which received a combination of fertilizer-15N+organic-material-N, results showed that the highest Ndff was occurred with mixture of leuceana and compost, whereas the lowest was induced with individual leuceana treatment. 15N recovery in shoots of barley ranged between 22.14 % to 82.16 %. The lowest occurred with application of mineral 15N alone and; the highest occurred where mineral 15N was mixed with compost or leucaena-compost mixture

  18. High Performance Infiltrated Backbones for Cathode-Supported SOFC's

    Gil, Vanesa; Kammer Hansen, Kent

    2014-01-01

    The concept of using highly ionic conducting backbones with subsequent infiltration of electronically conducting particles has widely been used to develop alternative anode-supported SOFC's. In this work, the idea was to develop infiltrated backbones as an alternative design based on cathode-supported...... printed symmetrical cells. Samples with LSM/YSZ composite and YSZ backbones made with graphite+PMMA as pore formers exhibited comparable Rp values to the screen printed LSM/YSZ cathode. This route was chosen as the best to fabricate the cathode supported cells. SEM micrograph of a cathode supported cell...... with infiltrated LSM nanoparticles is shown in Fig. 1. Figure 1. Cross section of LSM infiltrated cathode supported cell. [Formula]...

  19. Revision of the 15N(p,{\\gamma})16O reaction rate and oxygen abundance in H-burning zones

    Caciolli, A; Capogrosso, V; Bemmerer, D; Broggini, C; Corvisiero, P; Costantini, H; Elekes, Z; Formicola, A; Fulop, Zs; Gervino, G; Guglielmetti, A; Gustavino, C; Gyurky, Gy; Imbriani, G; Junker, M; Lemut, A; Marta, M; Menegazzo, R; Palmerini, S; Prati, P; Roca, V; Rolfs, C; Alvarez, C Rossi; Somorjai, E; Straniero, O; Strieder, F; Terrasi, F; Trautvetter, H P; Vomiero, A

    2011-01-01

    The NO cycle takes place in the deepest layer of a H-burning core or shell, when the temperature exceeds T {\\simeq} 30 {\\cdot} 106 K. The O depletion observed in some globular cluster giant stars, always associated with a Na enhancement, may be due to either a deep mixing during the RGB (red giant branch) phase of the star or to the pollution of the primordial gas by an early population of massive AGB (asymptotic giant branch) stars, whose chemical composition was modified by the hot bottom burning. In both cases, the NO cycle is responsible for the O depletion. The activation of this cycle depends on the rate of the 15N(p,{\\gamma})16O reaction. A precise evaluation of this reaction rate at temperatures as low as experienced in H-burning zones in stellar interiors is mandatory to understand the observed O abundances. We present a new measurement of the 15N(p,{\\gamma})16O reaction performed at LUNA covering for the first time the center of mass energy range 70-370 keV, which corresponds to stellar temperatures...

  20. Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design.

    Kevin Drew

    Full Text Available Peptidomimetics are classes of molecules that mimic structural and functional attributes of polypeptides. Peptidomimetic oligomers can frequently be synthesized using efficient solid phase synthesis procedures similar to peptide synthesis. Conformationally ordered peptidomimetic oligomers are finding broad applications for molecular recognition and for inhibiting protein-protein interactions. One critical limitation is the limited set of design tools for identifying oligomer sequences that can adopt desired conformations. Here, we present expansions to the ROSETTA platform that enable structure prediction and design of five non-peptidic oligomer scaffolds (noncanonical backbones, oligooxopiperazines, oligo-peptoids, [Formula: see text]-peptides, hydrogen bond surrogate helices and oligosaccharides. This work is complementary to prior additions to model noncanonical protein side chains in ROSETTA. The main purpose of our manuscript is to give a detailed description to current and future developers of how each of these noncanonical backbones was implemented. Furthermore, we provide a general outline for implementation of new backbone types not discussed here. To illustrate the utility of this approach, we describe the first tests of the ROSETTA molecular mechanics energy function in the context of oligooxopiperazines, using quantum mechanical calculations as comparison points, scanning through backbone and side chain torsion angles for a model peptidomimetic. Finally, as an example of a novel design application, we describe the automated design of an oligooxopiperazine that inhibits the p53-MDM2 protein-protein interaction. For the general biological and bioengineering community, several noncanonical backbones have been incorporated into web applications that allow users to freely and rapidly test the presented protocols (http://rosie.rosettacommons.org. This work helps address the peptidomimetic community's need for an automated and expandable

  1. Comparison of fast backbone dynamics at amide nitrogen and carbonyl sites in dematin headpiece C-terminal domain and its S74E mutant

    We perform a detailed comparison of fast backbone dynamics probed at amide nitrogen versus carbonyl carbon sites for dematin headpiece C-terminal domain (DHP) and its S74E mutant (DHPS74E). Carbonyl dynamics is probed via auto-correlated longitudinal rates and transverse C'/C'-Cα CSA/dipolar and C'/C'-N CSA/dipolar cross-correlated rates, while 15N data are taken from a previous study. Resulting values of effective order parameters and internal correlation times support the conclusion that C' relaxation reports on a different subset of fast motions compared to those probed at N-H bond vectors in the same peptide planes. 13C' order parameters are on the average 0.08 lower than 15N order parameters with the exception of the flexible loop region in DHP. The reduction of mobility in the loop region upon the S74E mutation can be seen from the 15N order parameters but not from the 13C order parameters. Internal correlation times at 13C' sites are on the average an order of magnitude longer than those at 15N sites for the well-structured C-terminal subdomains, while the more flexible N-terminal subdomains have more comparable average internal correlation times.

  2. Continuous field measurement of N2O isotopologues using FTIR spectroscopy following 15N addition

    Phillips, R. L.; Griffith, D. W.; Dijkstra, F. A.; Lugg, G.; Lawrie, R.; Macdonald, B.

    2012-12-01

    Anthropogenic additions of fertilizer nitrogen (N) have significantly increased the mole fraction of nitrous oxide (N2O) in the troposphere. Tracking the fate of fertilizer N and its transformation to N2O is important to advance knowledge of greenhouse gas emissions from soils. Transport and transformations are frequently studied using 15N labeling experiments, but instruments capable of continuous measurements of 15N-N2O at the surface of soil have only recently come to the fore. Our primary aim was to quantify emissions of N2O and the fraction of 15N emitted as N2O from an agricultural soil following 15N addition using a mobile Fourier Transform Infrared (FTIR) spectrometer. We set up a short-term field experiment on a coastal floodplain site near Nowra, New South Wales. We deployed an automated chamber system connected to a multi-pass cell (optical pathlength 24 m) and low resolution FTIR spectrometer to measure fluxes of all N2O isotopologues collected from five 0.25 m2 chambers every three hours. We measured N2O fluxes pre and post-application of 15N-labeled substrate as potassium nitrate (KNO3) or urea [CO(NH2)2] to the soil surface. Root mean square uncertainties for all isotopologue measurements were less than 0.3 nmol mol-1 for 1 minute average concentration measurements, and minimum detectable fluxes for each isotopologue were isotope ratio mass spectrometry. Approximately 1% (range 0.7 - 1.9%) of the total amount of 15N applied was emitted as N2O. Average fractions of 15N recovered in soil, root, shoot, and microbial biomass pools varied between trials but were approximately 0.4, 0.08, 0.1 and 0.03, respectively. The results indicate that the portable FTIR spectroscopic technique can effectively trace transfer of 15N to the atmosphere as N2O after 15N addition, allowing for powerful quantification of N2O emissions under field conditions.

  3. Fossil Fuel Combustion-Related Emissions Dominate Atmospheric Ammonia Sources during Severe Haze Episodes: Evidence from (15)N-Stable Isotope in Size-Resolved Aerosol Ammonium.

    Pan, Yuepeng; Tian, Shili; Liu, Dongwei; Fang, Yunting; Zhu, Xiaying; Zhang, Qiang; Zheng, Bo; Michalski, Greg; Wang, Yuesi

    2016-08-01

    The reduction of ammonia (NH3) emissions is urgently needed due to its role in aerosol nucleation and growth causing haze formation during its conversion into ammonium (NH4(+)). However, the relative contributions of individual NH3 sources are unclear, and debate remains over whether agricultural emissions dominate atmospheric NH3 in urban areas. Based on the chemical and isotopic measurements of size-resolved aerosols in urban Beijing, China, we find that the natural abundance of (15)N (expressed using δ(15)N values) of NH4(+) in fine particles varies with the development of haze episodes, ranging from -37.1‰ to -21.7‰ during clean/dusty days (relative humidity: ∼ 40%), to -13.1‰ to +5.8‰ during hazy days (relative humidity: 70-90%). After accounting for the isotope exchange between NH3 gas and aerosol NH4(+), the δ(15)N value of the initial NH3 during hazy days is found to be -14.5‰ to -1.6‰, which indicates fossil fuel-based emissions. These emissions contribute 90% of the total NH3 during hazy days in urban Beijing. This work demonstrates the analysis of δ(15)N values of aerosol NH4(+) to be a promising new tool for partitioning atmospheric NH3 sources, providing policy makers with insights into NH3 emissions and secondary aerosols for regulation in urban environments. PMID:27359161

  4. δ15N measurement of organic and inorganic substances by EA-IRMS: a speciation-dependent procedure.

    Gentile, Natacha; Rossi, Michel J; Delémont, Olivier; Siegwolf, Rolf T W

    2013-01-01

    Little attention has been paid so far to the influence of the chemical nature of the substance when measuring δ(15)N by elemental analysis (EA)-isotope ratio mass spectrometry (IRMS). Although the bulk nitrogen isotope analysis of organic material is not to be questioned, literature from different disciplines using IRMS provides hints that the quantitative conversion of nitrate into nitrogen presents difficulties. We observed abnormal series of δ(15)N values of laboratory standards and nitrates. These unexpected results were shown to be related to the tailing of the nitrogen peak of nitrate-containing compounds. A series of experiments were set up to investigate the cause of this phenomenon, using ammonium nitrate (NH(4)NO(3)) and potassium nitrate (KNO(3)) samples, two organic laboratory standards as well as the international secondary reference materials IAEA-N1, IAEA-N2-two ammonium sulphates [(NH(4))(2)SO(4)]-and IAEA-NO-3, a potassium nitrate. In experiment 1, we used graphite and vanadium pentoxide (V(2)O(5)) as additives to observe if they could enhance the decomposition (combustion) of nitrates. In experiment 2, we tested another elemental analyser configuration including an additional section of reduced copper in order to see whether or not the tailing could originate from an incomplete reduction process. Finally, we modified several parameters of the method and observed their influence on the peak shape, δ(15)N value and nitrogen content in weight percent of nitrogen of the target substances. We found the best results using mere thermal decomposition in helium, under exclusion of any oxygen. We show that the analytical procedure used for organic samples should not be used for nitrates because of their different chemical nature. We present the best performance given one set of sample introduction parameters for the analysis of nitrates, as well as for the ammonium sulphate IAEA-N1 and IAEA-N2 reference materials. We discuss these results considering the

  5. APPECT: An Approximate Backbone-Based Clustering Algorithm for Tags

    Zong, Yu; Xu, Guandong; Jin, Pin;

    2011-01-01

    resulting from the severe difficulty of ambiguity, redundancy and less semantic nature of tags. Clustering method is a useful tool to address the aforementioned difficulties. Most of the researches on tag clustering are directly using traditional clustering algorithms such as K-means or Hierarchical...... algorithm for Tags (APPECT). The main steps of APPECT are: (1) we execute the K-means algorithm on a tag similarity matrix for M times and collect a set of tag clustering results Z={C1,C2,…,Cm}; (2) we form the approximate backbone of Z by executing a greedy search; (3) we fix the approximate backbone as...

  6. Rivermouth alteration of agricultural impacts on consumer tissue δ(15N.

    James H Larson

    Full Text Available Terrestrial agricultural activities strongly influence riverine nitrogen (N dynamics, which is reflected in the δ(15N of riverine consumer tissues. However, processes within aquatic ecosystems also influence consumer tissue δ(15N. As aquatic processes become more important terrestrial inputs may become a weaker predictor of consumer tissue δ(15N. In a previous study, this terrestrial-consumer tissue δ(15N connection was very strong at river sites, but was disrupted by processes occurring in rivermouths (the 'rivermouth effect'. This suggested that watershed indicators of N loading might be accurate in riverine settings, but could be inaccurate when considering N loading to the nearshore of large lakes and oceans. In this study, the rivermouth effect was examined on twenty-five sites spread across the Laurentian Great Lakes. Relationships between agriculture and consumer tissue δ(15N occurred in both upstream rivers and at the outlets where rivermouths connect to the nearshore zone, but agriculture explained less variation and had a weaker effect at the outlet. These results suggest that rivermouths may sometimes be significant sources or sinks of N, which would cause N loading estimates to the nearshore zone that are typically made at discharge gages further upstream to be inaccurate. Identifying definitively the controls over the rivermouth effect on N loading (and other nutrients will require integration of biogeochemical and hydrologic models.

  7. Fate of 15N-urea applied to wheat-soybean succession crop

    The wheat crop in Sao Paulo State, Brazil, is fertilized with N, P and K. The rate of applied N (0 to 120 kg.ha-1) depends on the previous grown crop and the irrigation possibility. The response of wheat to rates and time of N application and the fate of N applied to irrigated wheat were studied during two years. Residual N recovery by soybean grown after the wheat was also studied. The maximum grain productivity was obtained with 92 kg.ha-1 of N. The efficiency of 15N-urea utilization ranged from 52% to 85%. The main loss of applied 15 N, 5% to 12% occurred as ammonia volatilized from urea applied on soil surface. The N loss by leaching even at the N rate of 135 kg.ha-1, was less than 1% of applied 15N, due to the low amount of rainfall during the wheat grown season and a controlled amount of irrigated water, that were sufficient to moisten only the wheat root zone. The residual 15 N after wheat harvest represents around 40% of N applied as urea: 20% in soil, 3% in wheat root system and 16% in the wheat straw. Soybean recovered less than 2% of the 15 N applied to wheat at sowing or at tillering stage. (author)

  8. Fate of {sup 15}N-urea applied to wheat-soybean succession crop

    Boaretto, Antonio Enedi; Trivelin, Paulo Cesar Ocheuze; Muraoka, Takashi [Centro de Energia Nuclear na Agricultura (CENA), Piracicaba, SP (Brazil)]. E-mail: aeboaret@cena.usp.br; pcotrive@cena.usp.br; muraoka@cena.usp.br; Spolidorio, Eduardo Scarpari [SN Centro de Pesquisa e Promocao de Sulfato de Amonio, Piracicaba, SP (Brazil)]. E-mail: sncentro@merconet.com.br; Freitas, Jose Guilherme de; Cantarella, Heitor [Instituto Agronomico de Campinas, SP (Brazil)]. E-mail: jfreitas@iac.sp.gov.br; hcantare@iac.sp.gov.br

    2004-07-01

    The wheat crop in Sao Paulo State, Brazil, is fertilized with N, P and K. The rate of applied N (0 to 120 kg.ha{sup -1}) depends on the previous grown crop and the irrigation possibility. The response of wheat to rates and time of N application and the fate of N applied to irrigated wheat were studied during two years. Residual N recovery by soybean grown after the wheat was also studied. The maximum grain productivity was obtained with 92 kg.ha{sup -1} of N. The efficiency of {sup 15}N-urea utilization ranged from 52% to 85%. The main loss of applied {sup 15} N, 5% to 12% occurred as ammonia volatilized from urea applied on soil surface. The N loss by leaching even at the N rate of 135 kg.ha{sup -1}, was less than 1% of applied {sup 15}N, due to the low amount of rainfall during the wheat grown season and a controlled amount of irrigated water, that were sufficient to moisten only the wheat root zone. The residual {sup 15} N after wheat harvest represents around 40% of N applied as urea: 20% in soil, 3% in wheat root system and 16% in the wheat straw. Soybean recovered less than 2% of the {sup 15} N applied to wheat at sowing or at tillering stage. (author)

  9. The 15N isotope to evaluate fertilizer nitrogen absorption efficiency by the coffee plant

    The use of the 15N label for agronomic research involving nitrogen (N) cycling and the fate of fertilizer-N is well established, however, in the case of long term experimentation with perennial crops like citrus, coffee and rubber tree, there are still shortcomings mainly due to large plant size, sampling procedures, detection levels and interferences on the system. This report tries to contribute methodologically to the design and development of 15N labeled fertilizer experiments, using as an example a coffee crop fertilized with 15N labeled ammonium sulfate, which was followed for two years. The N of the plant derived from the fertilizer was studied in the different parts of the coffee plant in order to evaluate its distribution within the plant and the agronomic efficiency of the fertilizer application practice. An enrichment of the fertilizer-N of the order of 2% 15N abundance was sufficient to study N absorption rates and to establish fertilizer-N balances after one and two years of coffee cropping. The main source of errors in the estimated values lies in the inherent variability among field replicates and not in the measurements of N contents and 15N enrichments of plant material by mass-spectrometry. (author)

  10. Incorporation of 15N-inorganic nitrogen into free-amino acids in germinating corn

    Incorporation of 15N-labeled compounds, (K15NO3) and (15NH4)2SO4, into free-amino acids was measured in germinating corn. Sterilized seeds of sweet corn (Choko No. 865) were sown on the filter papers soaked in 10 ml of the solution containing one of the labeled compounds (40 ppm N, 99 atom % excess) in petri dishes and germinated at 30 deg C. After 48 hours and 72 hours, 15N-incorporation was measured in 5 seedlings selected owing to uniform growth. A GC-MS was used for measuring the ratio of 15N isotopes present in free-amino acids. 15N incorporation into free-amino acids hardly occurred when corn was germinated in the solution containing K15NO3, which suggested that endogenous nitrogen was used during the early germination stage of corn when nitrate is present. Incorporation into amino acids was greater when corn was germinated in the medium containing (15NH4)2SO4, than the case of the solution containing K15NO3. When corn was germinated in the solution containing (15NH4)2SO4, assimilation of 15N into asparagine or aspartic acid was comparatively higher than that into the other amino acids, though the incorporation rate was low. Thus, in intact germinating corn, the hydrolyzed product of protein was utilized for germination with priority, and dependence on exogenous nitrogen was low. (Kaihara, S.)

  11. The {sup 15}N isotope to evaluate fertilizer nitrogen absorption efficiency by the coffee plant

    Fenilli, Tatiele A.B. [Universidade Regional de Blumenau, (FURB), SC (Brazil); Reichart, Klaus; Bacchi, Osny O.S.; Trivelin, Paulo Cesar Ocheuze [Centro de Energia Nuclear na Agricultura (CENA/USP), Piracicaba, SP (Brazil)]. E-mail: klaus@cena.usp.br; Dourado-Neto, Durval [Universidade de Sao Paulo (USP), Piracicaba, SP (Brazil). Escola Superior de Agricultura Luiz de Queiroz (ESALQ)

    2007-12-15

    The use of the {sup 15}N label for agronomic research involving nitrogen (N) cycling and the fate of fertilizer-N is well established, however, in the case of long term experimentation with perennial crops like citrus, coffee and rubber tree, there are still shortcomings mainly due to large plant size, sampling procedures, detection levels and interferences on the system. This report tries to contribute methodologically to the design and development of {sup 15}N labeled fertilizer experiments, using as an example a coffee crop fertilized with {sup 15}N labeled ammonium sulfate, which was followed for two years. The N of the plant derived from the fertilizer was studied in the different parts of the coffee plant in order to evaluate its distribution within the plant and the agronomic efficiency of the fertilizer application practice. An enrichment of the fertilizer-N of the order of 2% {sup 15}N abundance was sufficient to study N absorption rates and to establish fertilizer-N balances after one and two years of coffee cropping. The main source of errors in the estimated values lies in the inherent variability among field replicates and not in the measurements of N contents and {sup 15}N enrichments of plant material by mass-spectrometry. (author)

  12. Utilization of 15N in the sequence of mineral fertilizer - forage - animal - slurry - forage

    After systematic application of 15N-ammonium nitrate, the change of the dinuclidic composition and 15N quantity was studied by isotope analysis of several open systems in the sequence mineral fertilizer - (soil) - forage - (animal) - slurry - (soil) - forage. The relative 15N isotope frequency of 50 atom% in the mineral fertilizer declined to 12.2 to 21.4 atom% in the forage (beet, oats, hay) and went down to 3.15 atom% in the slurry of a dairy cow fed on this forage. Silage maize manured with the slurry of the dairy cow only showed 1.98 atom %, green oats grown after the silage maize on the same area was found to have 0.45 atom%. The 15N quantity of 104.5 g N in the fertilizer gradually decreased to 41.6 g N in the forage, 30.5 g N in the slurry and 22.6 g N in the silage maize. The causes discussed are 15N isotope dilution as qualitative factor and productive and unproductive N losses as quantitative factors. (author)

  13. Utilization of 15N-labelled urea in laying hens. 5

    In the series of experiments with labelled urea three colostomized laying hybrids were butchered after a six-day application of 1% urea with 96.06 atom-% 15N excess (15N') in the ration and another 2 days with a supplement of 1% unlabelled urea. Out of the individual samples from crop, gizzard, small intestine, caecum and rectum, the content of the small intestine and the caecum showed the highest labelling with > 1 atom-% 15N'. The TCA soluble fraction of the content of the gizzard was more highly and that of the intestines less labelled than the total nitrogen. The tissue of the gizzard is distinctly less labelled than the 'omasum system' and the small intestine. The atom-% 15N' of the oesophagus with crop and glandular stomach largely showed agreement in the individual hens with that of intestinal tissue and ranged between 0.71 and 0.89 atom-%. 2% of the 15N' supplemented with the urea could be recovered in the content and the tissue of the gastro-intestinal tract. (author)

  14. Grafting and carbonated irrigation water in transport of 15N and in the tomato production

    The effects of CO2 application through irrigation water, and of grafting in transport of 15N and in the tomato production, were studied. These treatments were arranged in a 2 x 2 factorial scheme (with and without CO2 in irrigation water and grafted and non-grafted tomato), in a completely randomized design, with four replications. The injection of CO2 into the water began at 34 days after transplant of seedlings (DAT) and continued for all irrigations. The application of the sulfate of ammonium with abundance in atoms of 15N of 3.13% in plants destined to analysis was done at 45 DAT when the plants were in the middle of fructification. After 14 days of fertilizer (15N) application the plants were harvested, washed, dried and sent for analysis of 15N in plant tissue. The results demonstrated that CO2 and the grafting did not alter the transport of 15N in the plant. The production of commercial fruits was larger when CO2 was applied in water. (author)

  15. STARD6 on steroids: solution structure, multiple timescale backbone dynamics and ligand binding mechanism

    Létourneau, Danny; Bédard, Mikaël; Cabana, Jérôme; Lefebvre, Andrée; LeHoux, Jean-Guy; Lavigne, Pierre

    2016-01-01

    START domain proteins are conserved α/β helix-grip fold that play a role in the non-vesicular and intracellular transport of lipids and sterols. The mechanism and conformational changes permitting the entry of the ligand into their buried binding sites is not well understood. Moreover, their functions and the identification of cognate ligands is still an active area of research. Here, we report the solution structure of STARD6 and the characterization of its backbone dynamics on multiple time-scales through 15N spin-relaxation and amide exchange studies. We reveal for the first time the presence of concerted fluctuations in the Ω1 loop and the C-terminal helix on the microsecond-millisecond time-scale that allows for the opening of the binding site and ligand entry. We also report that STARD6 binds specifically testosterone. Our work represents a milestone for the study of ligand binding mechanism by other START domains and the elucidation of the biological function of STARD6. PMID:27340016

  16. Preparation of 15N labelled protein sample by gene engineering technology

    Using the advanced multi-dimension heteronuclear pulses and isotope labelled protein technique, nuclear magnetic resonance spectroscopy has become an important tool in analysis of the solution conformation of protein. On the basis of the high level expression of a protein-trichosanthin in recombinant E.coli using DNA, 15N was used to label the protein, the 15N labelled trichosanthin was obtained by affinity chromatography on Ni-NTA agarose. Terminating pregnant effect in mice showed that this recombinant protein had the same activity as natural trichosanthin. A 1H-15N heteronuclear single-quantum coherence (HSQC) spectrum was obtained from an AM-500 NMR spectrometer, demonstrating that this method is suitable in preparing labelled protein sample for NMR

  17. Origin and tracing techniques of high 15N nitrogen compounds in industrial environments

    Effluents and process waters from various industrial plants were investigated for the 15N/14N isotope ratio in nitrate and ammonia. It was found that large isotope fractionation occurs in cases where ammonia is involved in gas-liquid phase changes. This feature was found to occur in two coke oven plants where ammonia gas is removed from a gas stream by solution in water, in an ammonia sulphate plant where ammonia gas is absorbed in sulphuric acid and in a water treatment plant where ammonia is removed from (high pH) water by blowing air through the process water. In all these cases 15N isotope enrichments (in the range of 10 to 30 per mille) occurred. These enrichments are in excess of those found naturally. Ammonia in such wastewaters essentially retains this high 15N content when it is converted to nitrate underground: which occurs rapidly under well-oxidised conditions. Nitrate is a fairly conservative tracer and its contamination in water can be followed readily. In the low recharge environment in the central parts of South Africa evidence of waste management practices of 10-20 years earlier were still quite evident using this isotopic label. The high 15N nitrate signal could be used to distinguish industrial nitrogen pollution from pollution by local sewage disposal systems. Vegetation that derives its nitrogen from such high 15N sources retains the isotope signature of its source. Grass and other annual plants then exhibit the isotope signature of the water of a specific year. Trees exhibit the isotope signature of deeper water, which shows the effects of longer term pollution events. The use of high 15N as tracer enables the source apportionment of nitrogen derived pollution in these specific circumstances. (author)

  18. Coral skeletal δ15N reveals isotopic traces of an agricultural revolution

    This study introduces a new method of tracing the history of nutrient loading in coastal oceans via δ15N analysis of organic nitrogen preserved in the skeleton of the massive Porites coral. Four coral cores were collected in Bali, Indonesia, from reefs exposed to high levels of fertilizers in agricultural run-off, from lagoonal corals impacted by sewage, and from a reef located 30 km offshore. Skeletal δ15N in the agriculturally exposed coral declined from 10.7 ± 0.4 per mille in 1970-1971, when synthetic fertilizers (-0.8 per mille ± 0.2 per mille ) were introduced to Bali, to a depleted 'anthropogenic' baseline of 3.5 per mille ± 0.4% in the mid-1990s. δ15N values were negatively correlated with rainfall, suggesting that marine δ15N lowers during flood-born influxes of waste fertilizers. Reef cores exposed to untreated sewage in terrestrial discharge were enriched (7.8 and 7.3 ± 0.4 per mille ), while the offshore core reflected background oceanic signals (6.2 ± 0.4 per mille). δ15N, N concentration, and C:N systematics indicate that the N isotopic composition of skeletal organic matter was generally well preserved over 30 years. We suggest that skeletal organic δ15N can serve as a recorder of past nitrogen sources. In Bali, this tracer suggests that the intensification of Western style agricultural practices since 1970 are contributing to the degradation of coastal coral reefs

  19. Modified micro-diffusion method for 15N-enriched soil solutions

    The preparation of solutions for determination of 15N/14N isotope ratios is described, with special reference to dilute samples. A micro-diffusion method has been simplified to be more suitable for rapid isotope-ratio determination in soil solutions collected in tensionics. Ammonia expelled during micro-diffusion is captured on acidified filter discs fixed to the caps of gas-tight vials. The discs are transferred to tin capsules for shipment to the Soil Science Unit for 15N-enrichment determination. (author)

  20. Optical $\\Lambda$ transitions and quantum computing in the $^{15}$N-V$^{-}$ Center in Diamond

    González, Gabriel; Leuenberger, Michael N.

    2009-01-01

    We present a thorough derivation of the excited state energy levels of the negatively charged $^{15}$N-V$^{-}$ center in diamond for the strong applied electric field case. We show that in the $^{15}$N-V$^{-}$ center a spin non-conserving two-photon $\\Lambda$ transition exists that is mediated by the hyperfine interaction, which provides the possibility to write quantum information. Using second order perturbation theory we obtain a $\\Lambda$ transition rate of the order of 10 MHz at room tem...

  1. 15N-urea tracing emission spectroscopy for detecting the infection of Helicobacter pylori

    Objective: To study a noninvasive and nonradioactive method, 15N-urea tracing emission spectroscopy, for detecting the Helicobacter pylori (Hp) infection. Methods: A group of 26 patients was tested with a method of 15N-urea tracing emission spectroscopy for detecting the Hp infection. Results: Taking the bacterial culture or (and) Gram stain as a standard, the specificity, sensitivity and positive predicting rate of the test were 81%, 89% and 84%, respectively. Conclusion: The method could be considered useful for clinical practice

  2. Constraints on oceanic N balance/imbalance from sedimentary 15N records

    M. A. Altabet

    2007-01-01

    Full Text Available According to current best estimates, the modern ocean's N cycle is in severe deficit. N isotope budgeting provides an independent geochemical constraint in this regard as well as the only means for past reconstruction. Overall, it is the relative proportion of N2 fixation consumed by water column denitrification that sets average oceanic δ15N under steady-state conditions. Several factors (conversion of organic N to N2, Rayleigh closed and open system effects likely reduce the effective fractionation factor (ε for water column denitrification to about half the inherent microbial value for εden. If so, the average oceanic δ15N of ~5‰ is consistent with a canonical contribution from water column denitrification of 50% of the source flux from N2 fixation. If an imbalance in oceanic N sources and sinks changes this proportion then a transient in average oceanic δ15N would occur. Using a simple model, changing water column denitrification by ±30% or N2 fixation by ±15% produces detectable (>1‰ changes in average oceanic δ15N over one residence time period or more with corresponding changes in oceanic N inventory. Changing sedimentary denitrification produces no change in δ15N but does change N inventory. Sediment δ15N records from sites thought to be sensitive to oceanic average δ15N all show no detectible change over the last 3 kyr or so implying a balanced marine N budget over the latest Holocene. A mismatch in time scales is the most likely meaningful interpretation of the apparent conflict with modern flux estimates. Decadal to centennial scale oscillations between net N deficit and net surplus may occur but on the N residence timescale of several thousand years, net balance is achieved in sum. However, sediment δ15N records from the literature covering the period since the last glacial maximum show excursions of up to several ‰ that are consistent with sustained N deficit during the deglaciation followed by readjustment

  3. Constraints on oceanic N balance/imbalance from sedimentary 15N records

    M. A. Altabet

    2006-07-01

    Full Text Available According to current best estimates, the modern ocean's N cycle is in severe deficit. N isotope budgeting provides an independent geochemical constraint in this regard as well as the only means for past reconstruction. Overall, it is the relative proportion of N2 fixation consumed by water column denitrification that sets average oceanic δ15N under steady-state conditions. Several factors (conversion of organic N to N2, Rayleigh closed and open system effects likely reduce the effective fractionation factor (ε for water column denitrification to about half the inherent microbial value for εden. If so, the average oceanic δ15N of ~5 is consistent with a canonical contribution from water column denitrification of 50% of the source flux from N2 fixation. If an imbalance in oceanic N sources and sinks changes this proportion then a transient in average oceanic δ15N would occur. Using a simple model, changing water column denitrification ±30% or N2 fixation by ±15% produces detectable (>1 changes in average oceanic δ15N over one residence time period or more with corresponding changes in oceanic N inventory. Changing sedimentary denitrification produces no change in δ15N but does change N inventory. Sediment δ15N records from sites thought to be sensitive to oceanic average δ15N all show no detectible change over the last 3 kyr or so implying a balanced marine N budget over the latest Holocene. A mismatch in time scales is the most likely meaningful interpretation of the apparent conflict with modern flux estimates. Decadal to centennial scale oscillations between net N deficit and net surplus may occur but on the N residence timescale of several thousand years, net balance is achieved in sum. However, sediment δ15N records from the literature covering the period since the last glacial maximum show excursions of up to several that are consistent with sustained N deficit during the deglaciation followed by readjustment and establishment of

  4. The Graphical Representation of the Digital Astronaut Physiology Backbone

    Briers, Demarcus

    2010-01-01

    This report summarizes my internship project with the NASA Digital Astronaut Project to analyze the Digital Astronaut (DA) physiology backbone model. The Digital Astronaut Project (DAP) applies integrated physiology models to support space biomedical operations, and to assist NASA researchers in closing knowledge gaps related to human physiologic responses to space flight. The DA physiology backbone is a set of integrated physiological equations and functions that model the interacting systems of the human body. The current release of the model is HumMod (Human Model) version 1.5 and was developed over forty years at the University of Mississippi Medical Center (UMMC). The physiology equations and functions are scripted in an XML schema specifically designed for physiology modeling by Dr. Thomas G. Coleman at UMMC. Currently it is difficult to examine the physiology backbone without being knowledgeable of the XML schema. While investigating and documenting the tags and algorithms used in the XML schema, I proposed a standard methodology for a graphical representation. This standard methodology may be used to transcribe graphical representations from the DA physiology backbone. In turn, the graphical representations can allow examination of the physiological functions and equations without the need to be familiar with the computer programming languages or markup languages used by DA modeling software.

  5. Determination of backbone chain direction of PDA using FFM

    Jo, Sadaharu; Okamoto, Kentaro; Takenaga, Mitsuru

    2010-01-01

    The effect of backbone chains on friction force was investigated on both Langmuir-Blodgett (LB) films of 10,12-heptacosadiynoic acid and the (0 1 0) surfaces of single crystals of 2,4-hexadiene-1,6-diol using friction force microscopy (FFM). It was observed that friction force decreased when the scanning direction was parallel to the [0 0 1] direction in both samples. Moreover, friction force decreased when the scanning direction was parallel to the crystallographic [1 0 2], [1 0 1], [1 0 0] and [1 0 1¯] directions in only the single crystals. For the LB films, the [0 0 1] direction corresponds to the backbone chain direction of 10,12-heptacosadiynoic acid. For the single crystals, both the [0 0 1] and [1 0 1] directions correspond to the backbone chain direction, and the [1 0 2], [1 0 0] and [1 0 1¯] directions correspond to the low-index crystallographic direction. In both the LB films and single crystals, the friction force was minimized when the directions of scanning and the backbone chain were parallel.

  6. The use of δ15N in assessing sewage stress on coral reefs

    While coral reefs decline, scientists argue, and effective strategies to manage land-based pollution lag behind the extent of the problem. There is need for objective, cost-effective, assessment methods. The measurement of stable nitrogen isotope ratios, δ15N, in tissues of reef organisms shows promise as an indicator of sewage stress. The choice of target organism will depend upon study purpose, availability, and other considerations such as conservation. Algae are usually plentiful and have been shown faithfully to track sewage input. The organic matrix of bivalve shells can provide time series spanning, perhaps, decades. Gorgonians have been shown to track sewage, and can provide records potentially centuries-long. In areas where baseline data are lacking, which is almost everywhere, δ15N in gorgonians can provide information on status and trends. In coral tissue, δ15N combined with insoluble residue determination can provide information on both sewage and sediment stress in areas lacking baseline data. In the developed world, δ15N provides objective assessment in a field complicated by conflicting opinions. Sample handling and processing are simple and analysis costs are low. This is a method deserving widespread application.

  7. Using a Macroalgal δ15N Bioassay to Detect Cruise Ship Waste Water Effluent Inputs

    Nitrogen stable isotopes are a powerful tool for tracking sources of N to marine ecosystems. I used green macroalgae as a bioassay organism to evaluate if the δ15N signature of cruise ship waste water effluent (CSWWE) could be detected in Skagway Harbor, AK. Opportunistic green...

  8. Determination of level widths in 15N using nuclear resonance fluorescence

    Szücs T.

    2015-01-01

    Full Text Available Level widths in 15N have been measured with the nuclear resonance fluorescence (NRF technique. Solid nitrogen compounds, bremsstrahlung, and HPGe detectors have been used as target, beam, and detectors, respectively. The preliminarily level widths are in agreement with the literature values, but more precise.

  9. An improved method for delta 15N measurements in ice cores

    M. Leuenberger

    2008-02-01

    Full Text Available The use of isotopic ratios of nitrogen gas (δ15N trapped in ice cores as a paleothermometer to characterise abrupt climate changes is becoming a widespread technique. The versatility of the technique could be enhanced, for instance in quantifying small temperature changes during the last glacial period in Antarctic ice cores, by using high precision methods. In this paper, we outline a method for measuring δ15N to a precision of 0.006permil (1σ, n=9 from replicate ice core samples. The high precision results from removing oxygen, carbon dioxide and water vapour from the air extracted from ice cores. The advantage of the technique is that it does not involve correction for isobaric interference due to CO+ ions. We also highlight the importance of oxygen removal from the sample, and how it influences δ15N measurements. The results show that a small amount of oxygen in the sample can be detrimental to achieving an optimum precision in δ15N measurements of atmospheric nitrogen trapped ice core samples.

  10. Pathways of nitrogen assimilation in cowpea nodules studied using 15N2 and allopurinol

    In the presence of 0.5 millimolar allopurinol (4-hydroxypyrazolo [3,4-d]pyrimidine), an inhibitor of NAD:xanthine oxidoreductase (EC 1.2.3.2), intact attached nodules of cowpea (vigna unguiculata L. Walp. cv Vita 3) formed [15N]xanthine from 15N2 at rates equivalent to those of ureide synthesis, confirming the direct assimilation of fixed nitrogen into purines. Xanthine accumulated in nodules and was exported in increasing amounts in xylem of allopurinol-treated plants. Other intermediates of purine oxidation, de novo purine synthesis, and ammonia assimilation did not increase and, over the time course of experiments (4 hours), allopurinol had no effect on nitrogenase (EC 1.87.99.2) activity. Negligible 15N -labeling of asparagine from 15N2 was observed, suggesting that the significant pool (up to 14 micromoles per gram of nodule fresh weight) of this amide in cowpea nodules was not formed directly from fixation but may have accumulated as a consequence of phloem delivery

  11. Experimental studies on porcine protein catabolism after thermic traumas using 15N

    Within studies on protein metabolism extensive third-degree burns were produced in pigs. During burn disease protein catabolism was determined by means of parenterally applied 15N-glycine and the improvement of the negative total N balance as well as modes of application of amino acids and proteins especially albumins are discussed

  12. Interregional training course on the use of 15N in soil science and plant nutrition

    In trials under greenhouse conditions the action of herbicides (2,4-D, Atrazine, Dicamba, Lenacil) on the nitrogen metabolism (total fertilizer nitrogen uptake, incorporation of fertilizer into composition of nitrogeneous substances) of sensitive and resistant plants (pea, maize, spring wheat, weeds) was studied by means of 15N-labelled fertilizer nitrogen. (author)

  13. Recovery of 15N-urea in soil-plant system of tanzania grass pasture

    The economic attractiveness and negative environmental impact of nitrogen (N) fertilization in pastures depend on the N use efficiency in the soil-plant system. However, the recovery of urea-15N by Panicum maximum cv. Tanzania pastures, one of the most widely used forage species in intensified pastoral systems, is still unknown. This experiment was conducted in a randomized complete block design with four treatments (0, 40, 80 and 120 kg ha-1 of N-urea) and three replications, to determine the recovery of 15N urea by Tanzania grass. Forage production, total N content and N yield were not affected by fertilization (p > 0.05), reflecting the high losses of applied N under the experimental conditions. The recovery of 15N urea (% of applied N) in forage and roots was not affected by fertilization levels (p > 0.05), but decreased exponentially in the soil and soil-plant system (p 15N (kg ha-1) in forage and roots (15 to 30 cm) increased with increasing urea doses (p < 0.05). (author)

  14. δ15N as a proxy for historic anthropogenic nitrogen loading in Charleston Harbor, SC, USA

    Payne, T. N.; Andrus, C. F. T.

    2015-12-01

    Bivalve shell geochemistry can serve as a useful indicator of changes in coastal environments. There is increasing interest in developing paleoenvironmental proxies from mollusk shell organic components. Numerous studies have focused on how the δ15N obtained from bivalve tissues can be used to trace present-day wastewater input into estuaries. However, comparatively little attention has been paid to tracing the impact of anthropogenic nitrogen loading into estuaries over time. By measuring historic levels of δ15N in the organic fraction of oyster shells (Crassostrea virginica) from archaeological sites around Charleston Harbor and comparing those levels to the δ15N content of modern shells, it is possible to assess how nitrogen has fluctuated historically in the area. Whole-shell samples from the Late Archaic Period (~3000-4000 BP, Late Woodland Period (~1400-800 BP), 18th and 19th centuries, and modern controls were measured for %N and d15N. Evidence of increased anthropogenic input of N is expected to begin in the early historic period based on similar analysis in Chesapeake Bay. More ancient samples may give insight into baseline conditions prior to recent population growth and industrialization. This information could help understand how large-scale anthropogenic nitrogen loading has affected coastal ecosystems over time and guide future remediation. Furthermore, this project will help refine and improve this novel proxy of past environmental conditions.

  15. Impact of seaweed beachings on dynamics of δ15N isotopic signatures in marine macroalgae

    Highlights: • Two coastal sites (COU, GM) in the Bay of Seine affected by summer seaweed beachings. • The same temporal dynamics of the algal δ15N at the two sites. • N and P concentrations in seawater of the two sites dominated by riverine sources. • A coupling between seaweed beachings and N sources of intertidal macroalgae. - Abstract: A fine-scale survey of δ15N, δ13C, tissue-N in seaweeds was conducted using samples from 17 sampling points at two sites (Grandcamp-Maisy (GM), Courseulles/Mer (COU)) along the French coast of the English Channel in 2012 and 2013. Partial triadic analysis was performed on the parameter data sets and revealed the functioning of three areas: one estuary (EstA) and two rocky areas (GM∗, COU∗). In contrast to oceanic and anthropogenic reference points similar temporal dynamics characterized δ15N signatures and N contents at GM∗ and COU∗. Nutrient dynamics were similar: the N-concentrations in seawater originated from the River Seine and local coastal rivers while P-concentrations mainly from these local rivers. δ15N at GM∗ were linked to turbidity suggesting inputs of autochthonous organic matter from large-scale summer seaweed beachings made up of a mixture of Rhodophyta, Phaeophyta and Chlorophyta species. This study highlights the coupling between seaweed beachings and nitrogen sources of intertidal macroalgae

  16. Incorporation of 15N-labelled fertilizer nitrogen into wheat grain proteins during grain development

    The aim of our experiments was to study the incorporation of 15N-labelled fertilizer nitrogen into winter wheat (Triticum aestivum L.) grain and its protein fractions during grain development. The microplot N fertilization experiments were carried out on a eutric Cambisol of medium N status in Keszthely (Hungary). (author)

  17. Applications of stable isotopes of 2H, 13C and 15N to clinical problems

    The function of the Argonne Program is to provide synthetic, analytical instrumental capability in a core facility for the clinical investigator who needs to use 2H, 13C, or 15N labelled compounds for metabolic or clinical research on pregnant women, newborn infants, young children, or for mass screening. To carry out such application development, there were six stages which were recurrent steps in every application. Five fundamental strategies should be adopted to establish the use of stable isotopes in clinical work. The instrument required for measurements was a combined gas chromatograph-mass spectrometer, and its use was schematically illustrated. Some of the successful experiences with compounds labelled by stable isotopes, such as deuterium labelled chenodeoxycholic acid, and respective 13C and 15N-labelled glycine were described. Deutrium labelled bile acid enabled easy and safe determination of the size of the bile acid pool and the replacement rate, providing clearer diagnoses for cholestatic liver disease and gallstones. 13C and 15N labelled compounds were used in clinical studies, of children with genetic disorders of amino acid metabolism, i.e., non ketotic hyperflycinemia, B12-responsive methyl malonic acidemia, and Lesch-Nyhan syndrome. 15N-labelled glycine was also studied in a child with Lesch-Nyhan syndrome. (Mukohata, S.)

  18. Carbon-rich presolar grains from massive stars. Subsolar 12C/13C and 14N/15N ratios and the mystery of 15N

    Pignatari, M; Hoppe, P; Jordan, C J; Gibson, B K; Trappitsch, R; Herwig, F; Fryer, C; Hirschi, R; Timmes, F X

    2015-01-01

    Carbon-rich grains with isotopic anomalies compared to the Sun are found in primitive meteorites. They were made by stars, and carry the original stellar nucleosynthesis signature. Silicon carbide grains of Type X and C, and low-density graphites condensed in the ejecta of core-collapse supernovae. We present a new set of models for the explosive He shell and compare them with the grains showing 12C/13C and 14N/15N ratios lower than solar. In the stellar progenitor H was ingested into the He shell and not fully destroyed before the explosion. Different explosion energies and H concentrations are considered. If the SN shock hits the He-shell region with some H still present, the models can reproduce the C and N isotopic signatures in C-rich grains. Hot-CNO cycle isotopic signatures are obtained, including a large production of 13C and 15N. The short-lived radionuclides 22Na and 26Al are increased by orders of magnitude. The production of radiogenic 22Ne from the decay of 22Na in the He shell might solve the pu...

  19. Refinement of the protein backbone angle {psi} in NMR structure calculations

    Sprangers, R.; Bottomley, M.J.; Linge, J.P.; Schultz, J.; Nilges, M.; Sattler, M. [European Molecular Biology Laboratory (Germany)

    2000-01-15

    Cross-correlated relaxation rates involving the C{sup {alpha}}-H{sup {alpha}} dipolar interaction and the carbonyl (C') chemical shift anisotropy (CSA) have been measured using two complementary 3D experiments. We show that the protein backbone angle {psi} can be directly refined against such cross-correlated relaxation rates ({gamma}{sup H{alpha}}{sup C{alpha}}{sup ,C'}) and the three-bond H/D isotope effect on the C{sup {alpha}} chemical shifts ({sup 3}{delta}C{sup {alpha}}{sub (ND)}). By simultaneously using both experimental parameters as restraints during NMR structure calculations, a unique value for the backbone angle {psi} is defined. We have applied the new refinement method to the {alpha}-Spectrin SH3 domain (a {beta}-sheet protein) and to the Sgs1p HRDC domain (an {alpha}-helical protein) and show that the quality of the NMR structures is substantially improved, judging from the atomic coordinate precision and the Ramachandran map. In addition, the {psi}-refined NMR structures of the SH3 domain deviate less from the 1.8 A crystal structure, suggesting an improved accuracy. The proposed refinement method can be used to significantly improve the quality of NMR structures and will be applicable to larger proteins.

  20. Studies of the endogeneous N metabolism in 15N-labelled pigs. 2

    4 pigs were labelled with 15N-ammonium salt over a period of 10 days in the feeding of a fishmeal diet (1), a fishmeal diet + partly hydrolyzed straw meal (2), a field bean diet (3) and a field bean diet + partly hydrolyzed straw meal (4). The 14N-amino acids and the 15N-amino acids excreted in feces showed highly significant correlation coefficient with the increasing content of crude fiber in the diets, which amounted to 3.0, 5.3, 10.0 and 12.1% in the dry matter. The following sequence was established for the growth angle of the essential 14N-amino acids: Leu, Lys, Arg, Thr, Phe, Ile, Val, His and of the 15N-amino acids: Lys, Arg, Val, Leu, Ile, Thr, Phe and His. As Lys, His and Thr cannot incorporate 15N in transamination reactions in the intermediate metabolism, their level of labelling was considerable in case of diet 4. Nevertheless, tan α is highest for 15N-Lys and lowest for 15N-His. This means that His in contrast to Lys, parallel to increased synthesis, is also increasingly decomposed in the large intestine. In contrast to this, proline was not labelled with 15N even with the highest content of crude fiber in the diet. Despite this, 14N-proline excretion, next to glutamic acid, increased most with the growing content of crude fiber in the diet. Due to the hydrophilic character of glutamic acid and the increased water influx in the large intestine and the increased content of crude fiber in the diet, a growing proline transport parallel to the increased influx of crude fiber and water must be assumed. If the growth angle tan α for the excretion of 14N-amino acids is ascertained regressively for a crude fiber content of diet of 10 %, one can prove from the proportion of the amino acids and a comparison from literature for fecal bacteria and ileum digesta that the amino acid composition for this measuring point largely corresponds to that of bacterial protein. (author)

  1. Fertilizer 15N balance in a coffee cropping system: a case study in Brazil

    Knowledge about the fate of fertilizer nitrogen in agricultural systems is essential for the improvement of management practices in order to maximize nitrogen (N) recovery by the crop and reduce N losses from the system to a minimum. This study involves fertilizer management practices using the 15N isotope label applied in a single rate to determine the fertilizer-N balance in a particular soil-coffee-atmosphere system and to deepen the understanding of N plant dynamics. Five replicates consisting of plots of about 120 plants each were randomly defined within a 0.2 ha coffee plantation planted in 2001, in Piracicaba, SP, Brazil. Nine plants of each plot were separated in sub-plots for the 15N balance studies and treated with N rates of 280 and 350 kg ha-1 during 2003/2004 and 2004/ 2005, respectively, both of them as ammonium sulfate enriched to a 15N abundance of 2.072 atom %. Plant shoots were considered as separate parts: the orthotropic central branch, productive branches, leaves of productive branches, vegetative branches, leaves of vegetative branches and fruit. Litter, consisting of dead leaves accumulated below the plant canopy, was measured by the difference between leaves at harvest and at the beginning of the following flowering. Roots and soil were sampled down to a depth of 1.0 at intervals of 0.2 m. Samples from the isotopic sub-plots were used to evaluate total N and 15N, and plants outside sub-plots were used to evaluate dry matter. Volatilization losses of NH3 were estimated using special collectors. Leaching of fertilizer-N was estimated from deep drainage water fluxes and 15N concentrations of the soil solution at 1 m soil depth. At the end of the 2-year evaluation, the recovery of 15N applied as ammonium sulfate was 19.1 % in aerial plant parts, 9.4 % in the roots, 23.8 % in the litter, 26.3 % in the fruit and 12.6 % remaining in the 0-1.0 m soil profile. Annual leaching and volatilization losses were very small (2.0 % and 0.9 %, respectively

  2. Variable δ(15)N diet-tissue discrimination factors among sharks: implications for trophic position, diet and food web models.

    Olin, Jill A; Hussey, Nigel E; Grgicak-Mannion, Alice; Fritts, Mark W; Wintner, Sabine P; Fisk, Aaron T

    2013-01-01

    The application of stable isotopes to characterize the complexities of a species foraging behavior and trophic relationships is dependent on assumptions of δ(15)N diet-tissue discrimination factors (∆(15)N). As ∆(15)N values have been experimentally shown to vary amongst consumers, tissues and diet composition, resolving appropriate species-specific ∆(15)N values can be complex. Given the logistical and ethical challenges of controlled feeding experiments for determining ∆(15)N values for large and/or endangered species, our objective was to conduct an assessment of a range of reported ∆(15)N values that can hypothetically serve as surrogates for describing the predator-prey relationships of four shark species that feed on prey from different trophic levels (i.e., different mean δ(15)N dietary values). Overall, the most suitable species-specific ∆(15)N values decreased with increasing dietary-δ(15)N values based on stable isotope Bayesian ellipse overlap estimates of shark and the principal prey functional groups contributing to the diet determined from stomach content analyses. Thus, a single ∆(15)N value was not supported for this speciose group of marine predatory fishes. For example, the ∆(15)N value of 3.7‰ provided the highest percent overlap between prey and predator isotope ellipses for the bonnethead shark (mean diet δ(15)N = 9‰) whereas a ∆(15)N value shark (mean diet δ(15)N = 15‰). These data corroborate the previously reported inverse ∆(15)N-dietary δ(15)N relationship when both isotope ellipses of principal prey functional groups and the broader identified diet of each species were considered supporting the adoption of different ∆(15)N values that reflect the predators' δ(15)N-dietary value. These findings are critical for refining the application of stable isotope modeling approaches as inferences regarding a species' ecological role in their community will be influenced with consequences for conservation and

  3. Variable δ(15N diet-tissue discrimination factors among sharks: implications for trophic position, diet and food web models.

    Jill A Olin

    Full Text Available The application of stable isotopes to characterize the complexities of a species foraging behavior and trophic relationships is dependent on assumptions of δ(15N diet-tissue discrimination factors (∆(15N. As ∆(15N values have been experimentally shown to vary amongst consumers, tissues and diet composition, resolving appropriate species-specific ∆(15N values can be complex. Given the logistical and ethical challenges of controlled feeding experiments for determining ∆(15N values for large and/or endangered species, our objective was to conduct an assessment of a range of reported ∆(15N values that can hypothetically serve as surrogates for describing the predator-prey relationships of four shark species that feed on prey from different trophic levels (i.e., different mean δ(15N dietary values. Overall, the most suitable species-specific ∆(15N values decreased with increasing dietary-δ(15N values based on stable isotope Bayesian ellipse overlap estimates of shark and the principal prey functional groups contributing to the diet determined from stomach content analyses. Thus, a single ∆(15N value was not supported for this speciose group of marine predatory fishes. For example, the ∆(15N value of 3.7‰ provided the highest percent overlap between prey and predator isotope ellipses for the bonnethead shark (mean diet δ(15N = 9‰ whereas a ∆(15N value < 2.3‰ provided the highest percent overlap between prey and predator isotope ellipses for the white shark (mean diet δ(15N = 15‰. These data corroborate the previously reported inverse ∆(15N-dietary δ(15N relationship when both isotope ellipses of principal prey functional groups and the broader identified diet of each species were considered supporting the adoption of different ∆(15N values that reflect the predators' δ(15N-dietary value. These findings are critical for refining the application of stable isotope modeling approaches as inferences regarding a species

  4. Effect of applying wheat stubble on preservation and utilization of n-fertilizer by 15N trace technique

    By using 15N trace technique, the effect of applying wheat stubble on the preservation and utilization rate of 15N- ammonium sulphate have been studied. The abundance of (15NH4)2SO4 fertilizer was 8.92%. After three years pot test and field plot test, the results showed that the yields with '15N+mulching' and '15N+incorporating' treated were increased by 5.4∼30.0% for spring wheat and millet(pot test), and 18∼23% for winter wheat and summer corn(field plot test), as compared with only '15N' treatment. The results of 15N-fertilizer labelled tests showed that the utilization rates of 15N-fertilizer treated by '15N+mulching' for cropping seasons were 57.8%, 65.8%, 36.6% and 8.5% respectively. These were increased 3.7%, 10.2%, 21.5% and 2.8% as compared with only '15N' treatment. Comparing with only '15N'treatment, the N leached off by percolation water was decreasing 50%, the loss of N caused by volatilization was decreasing 30.3% and the N in humus was increasing 21.1%. All of these proved that the applying of wheat stubble in different mode would adjust and control the activation of microbe in the soil, and the preservation and utilization rate of fertilizer in the soul would be increased

  5. Application time of nitrogen fertilizer 15N by a potato crop (Solanum Tuberosum L.)

    This study was performed at the ''San Jorge'' experimental farm of the Instituto Colombiano Agropecuario (ICA), Bogota, Colombia. The study was performed to investigate the effect of timing of application of nitrogen fertilizer on the productivity of, and the efficiency of utilization of 15N-labelled fertilizer by, a potato crop (Solanum tuberosum L.), cv. Tequendama. The crop was fertilized with 100, 200 and 100 Kg/ha-1 of N, P2O5 and K2O respectively. The N fertilizers were either added as 15N labelled urea (2.955 at.% 15N excess) or as labelled ammonium sulphate (2.071 at.% 15N excess). In all treatments with nitrogen, a total of 100 Kg N ha-1 was added, but the nitrogen was added either in two or three split doses (only one dose being labelled with 15N) at the following times: at planting, 35 days after emergence (DAE) and/or 60 DAE. It was found that: a) Nitrogen fertilization increased tuber production from 24 to 43 t/ha-1; b) The tubers constituted approximately 80% of total plant dry matter and 70% of the total nitrogen and fertilizer N accumulated by the plant; c) The fertilizer use efficiency varied between 49 and 68%, and the highest efficiency occurred when the nitrogen was split in three doses; d) The urea and ammonium sulphate gave similar results in all parameters evaluated; e) When the total nitrogen difference method was applied to interpretation of the results the fertilizer use efficiency was overestimated by 15 to 30%

  6. Araucaria cunninghamii Seedling Response to Different Forms and Rates of 15N-Labelled Fertiliser

    T.J.BLUMFIELD; XU Zhi-Hong

    2006-01-01

    Nitrogenous fertilisers are under consideration for promoting the growth of nursery-reared hoop pine (Araucaria cunninghamii Aiton ex A. Cunn) seedlings in the establishment phase of second rotation (2R) plantations. Using 15Nlabelled fertilisers, we investigated the effect of different forms (ammonium sulphate, ammonium nitrate, potassium nitrate and urea) and rates of application (0, 150 and 300 mg N kg-1 dried soil) of fertilisers on the growth, 15N recovery and carbon isotope composition (δ13C) of hoop pine seedlings in a 12-month glasshouse trial in southeast Queensland,Australia. The 15N-labelled fertilisers were applied to nursery-reared hoop pine seedlings, which were then grown in pots,containing ca. 1.2 kg dried soil, under well watered conditions for 12 months. Four seedlings from each treatment were harvested at 4-month intervals, divided into roots, stem and foliage, with a further subdivision for new and old foliage,and then analysed for 15N, total N, δ13C and total C. There was no significant response in the seedling growth to the form or rate of application of nitrogen (N) fertiliser within the 12-month period, indicating that the seedlings did not experience N deficiency when grown on second rotation hoop pine soils. While the combined 15N recovery from soil and plant remained at around 70% throughout the experiment, the proportion of 15N recovered from the plants increasing steadily over time. Nitrate containing fertilisers at 150 mg N kg-1 soil gradually increased seedling foliage δ13C over the 12-month period, indicating an increase in seedling water use efficiency.

  7. Bradyrhizobium strain and the 15N natural abundance quantification of biological N2 fixation in soybean

    In commercial plantations of soybean in both the Southern and the Cerrado regions, contributions from biological nitrogen fixation (BNF) are generally proportionately high. When using the 15N natural abundance technique to quantify BNF inputs, it is essential to determine, with accuracy, the 15N abundance of the N derived from BNF (the 'B' value). This study aimed to determine the effect of four recommended strains of Bradyrhizobium spp. (two B. japonicum and two B. elkanii) on the 'B' value of soybean grown in pots in an open field using an equation based on the determination of δ15N natural abundance in a non-labelled soil, and estimate of the contribution of BNF derived from the use of 15N-isotope dilution in soils enriched with 15N. To evaluate N2 fixation by soybean, three non-N2-fixing reference crops were grown under the same conditions. Regardless of Bradyrhizobium strain, no differences were observed in dry matter, nodule weight and total N between labelled and non-labelled soil. The N2 fixation of the soybeans grown in the two soil conditions were similar. The mean 'B' values of the soybeans inoculated with the B. japonicum strains were -1.84 per mille and -0.50 per mille, while those inoculated with B. elkanii were -3.67 per mille and -1.0 per mille, for the shoot tissue and the whole plant, respectively. Finally, the 'B' value for the soybean crop varied considerably in function of the inoculated Bradyrhizobium strain, being most important when only the shoot tissue was utilised to estimate the proportion of N in the plant derived from N2 fixation. (author)

  8. Distribution of 15N-labeled urea injected into field-grown corn plants

    Nitrogen (N) assimilate supply to developing corn (Zea mays L.) ears plays a critical role in grain dry weight accumulation. The use of stem-perfused/injected 15N labeled compounds to determine the effects of an artificial N source on the subsequent distribution of injected N and grain weight of field-grown corn plants has not been reported previously. Our objective was to assess the distribution of N added via an artificial source. Three soil N fertilizer levels (0, 180, and 270 kg N ha-1) and three N solutions (distilled water control and 15N enriched urea at 15 and 30 mM N) were arranged in a split-plot design. Three N concentrations were injected using a pressurized stem injection technique. The injection started fifteen days after silking and continued until immediately prior to plant physiological maturity. The average uptake volume was 256 mL over the 30-day injection period. The N supplied via injection represented 1.5 to 3% of the total plant N. Neither soil applied N fertilizer nor injected N altered dry matter distribution among plant tissues. As the concentration of N in the injected solutions increased, N concentrations increased in the grain and upper stalks, and % 15N atom excess in ear+1 leaves and leaves increased. The relative degree of 15N enrichment for each of the tissues measured was injected internode grain upper stalks leaves lower stalks cob husk ear + 1 leaf ear leaf. This study indicated that the exogenous N supplied via stem-injection, was incorporated into all the measured plant parts, although not uniformly. The distribution of the injected 15N was affected both by the proximity of sinks to the point of injection and the strength of the various sinks

  9. Evaluating δ(15)N-body size relationships across taxonomic levels using hierarchical models.

    Reum, Jonathan C P; Marshall, Kristin N

    2013-12-01

    Ecologists routinely set out to estimate the trophic position of individuals, populations, and species composing food webs, and nitrogen stable isotopes (δ(15)N) are a widely used proxy for trophic position. Although δ(15)N values are often sampled at the level of individuals, estimates and confidence intervals are frequently sought for aggregations of individuals. If individual δ(15)N values are correlated as an artifact of sampling design (e.g., clustering of samples in space or time) or due to intrinsic groupings (e.g., life history stages, social groups, taxonomy), such estimates may be biased and exhibit overly optimistic confidence intervals. However, these issues can be accommodated using hierarchical modeling methods. Here, we demonstrate how hierarchical models offer an additional quantitative tool for investigating δ(15)N variability and we explicitly evaluate how δ(15)N varies with body size at successively higher levels of taxonomic aggregation in a diverse fish assemblage. The models take advantage of all available data, better account for uncertainty in parameters estimates, may improve inferences on coefficients corresponding to groups with small to moderate sample sizes, and partition variation across model levels, which provides convenient summaries of the 'importance' of each level in terms of unexplained heterogeneity in the data. These methods can easily be applied to diet-based studies of trophic position. Although hierarchical models are well-understood and established tools, their benefits have yet to be fully reaped by stable isotope and food web ecologists. We suggest that hierarchical models can provide a robust framework for conceptualizing and statistically modeling trophic position at multiple levels of aggregation. PMID:23812110

  10. Influence of open ocean nitrogen supply on the skeletal δ15N of modern shallow-water scleractinian corals

    Wang, Xingchen T.; Sigman, Daniel M.; Cohen, Anne L.; Sinclair, Daniel J.; Sherrell, Robert M.; Cobb, Kim M.; Erler, Dirk V.; Stolarski, Jarosław; Kitahara, Marcelo V.; Ren, Haojia

    2016-05-01

    The isotopic composition of skeleton-bound organic nitrogen in shallow-water scleractinian corals (hereafter, CS-δ15N) is an emerging tool for studying the marine nitrogen cycle in the past. The CS-δ15N has been shown to reflect the δ15N of nitrogen (N) sources to corals, with most applications to date focusing on the anthropogenic/terrestrial N inputs to reef environments. However, many coral reefs receive their primary N sources from the open ocean, and the CS-δ15N of these corals may provide information on past changes in the open ocean regional and global N cycle. Using a recently developed persulfate/denitrifier-based method, we measured CS-δ15N in modern shallow-water scleractinian corals from 8 sites proximal to the open ocean. At sites with low open ocean surface nitrate concentrations typical of the subtropics and tropics, measured CS-δ15N variation on seasonal and annual timescales is most often less than 2‰. In contrast, a broad range in CS-δ15N (of ∼10‰) is measured across these sites, with a strong correlation between CS-δ15N and the δ15N of the deep nitrate supply to the surface waters near the reefs. While CS-δ15N can be affected by other N sources as well and can vary in response to local reef conditions as well as coral/symbiont physiological changes, this survey indicates that, when considering corals proximal to the open ocean, the δ15N of the subsurface nitrate supply to surface waters drives most of the CS-δ15N variation across the global ocean. Thus, CS-δ15N is a promising proxy for reconstructing the open ocean N cycle in the past.

  11. Use of 15N/14N Ratio to Evaluate the Sources of Nitrate Pollution in Surface and Groundwaters in the Upper Orontes Basin (Central Syria)

    This work represents the results of using of 15N technique in the evaluation and interpretation of nitrate pollution sources of surface and groundwaters in the Upper Orontes Basin (Central Syria). Based on this method, it was possible to distinguish between two groups of water bodies: 1) the group of fresh and non polluted water, which effectively reflects natural mineralization in nitrogen, such as the waters in the Upper Orontes River, the Qattineh Lake in its western and southern parts, as well as the Al-Qoussier well; 2) the group of polluted water, such as the waters in the other sampling sites. The chemical and isotopic 15N characteristics of this group reflect the impact of different intensities of pollution processes, which could mainly be derived from anthropogenic source. The intensity of this source was maximum in the Al-Domineh well, which was practically close to a sewage sink. (author)

  12. Polystyrene Backbone Polymers Consisting of Alkyl-Substituted Triazine Side Groups for Phosphorescent OLEDs

    Beatrice Ch. D. Salert

    2012-01-01

    Full Text Available This paper describes the synthesis of new electron-transporting styrene monomers and their corresponding polystyrenes all with a 2,4,6-triphenyl-1,3,5-triazine basic structure in the side group. The monomers differ in the alkyl substitution and in the meta-/paralinkage of the triazine to the polymer backbone. The thermal and spectroscopic properties of the new electron-transporting polymers are discussed in regard to their chemical structures. Phosphorescent OLEDs were prepared using the obtained electron-transporting polymers as the emissive layer material in blend systems together with a green iridium-based emitter 13 and a small molecule as an additional cohost with wideband gap characteristics (CoH-001. The performance of the OLEDs was characterized and discussed in regard to the chemical structure of the new electron-transporting polymers.

  13. Sequential backbone resonance assignments of the E. coli dihydrofolate reductase Gly67Val mutant: folate complex.

    Puthenpurackal Narayanan, Sunilkumar; Maeno, Akihiro; Wada, Yuji; Tate, Shin-Ichi; Akasaka, Kazuyuki

    2016-04-01

    Occasionally, a mutation in an exposed loop region causes a significant change in protein function and/or stability. A single mutation Gly67Val of E. coli dihydrofolate reductase (DHFR) in the exposed CD loop is such an example. We have carried out the chemical shift assignments for H(N), N(H), C(α) and C(β) atoms of the Gly67Val mutant of E. coli DHFR complexed with folate at pH 7.0, 35 °C, and then evaluated the H(N), N(H), C(α) and C(β) chemical shift changes caused by the mutation. The result indicates that, while the overall secondary structure remains the same, the single mutation Gly67Val causes site-specific conformational changes of the polypeptide backbone restricted around the adenosine-binding subdomain (residues 38-88) and not in the distant catalytic domain. PMID:26482924

  14. Constructing Battery-Aware Virtual Backbones in Wireless Sensor Networks

    Chi Ma; Yuanyuan Yang; Zhenghao Zhang

    2007-01-01

    A critical issue in battery-powered sensor networks is to construct energy efficient virtual backbones for network routing. Recent study in battery technology reveals that batteries tend to discharge more power than needed and reimburse the over-discharged power if they are recovered. In this paper we first provide a mathematical battery model suitable for implementation in sensor networks. We then introduce the concept of battery-aware connected dominating set (BACDS) and show that in gener...

  15. Primerjava JavaScript ogrodij Angular, Backbone in Ember

    Simin, Matija

    2016-01-01

    Diplomsko delo primerja tri JavaScript ogrodja za razvoj spletnih aplikacij, in sicer AngularJS, Ember.js in Backbone.js. V okviru dela smo primerjali njihovo implementacijo MVC arhitekturnega modela ali različice le-tega. Poleg implementacije MVC arhitekturnega modela smo primerjali njihove funkcionalnosti in lastnosti, kot so sistem predlog, implementacija usmerjevalnika, komunikacija s strežnikom, podatkovne povezave, prilagodljivosti, velikost in aktivnost skupnosti, kvaliteta obstoje...

  16. Comparison of JavaScript frameworks, Angular, Backbone, and Ember

    Simin, Matija

    2016-01-01

    The thesis compares three JavaScript frameworks for developing web applications: AngularJS, Ember.js and Backbone.js. In the thesis we compared their implementation of the MVC design pattern and their subversions. Besides their implementation of MVC design pattern we compared their functionalities and features, such as templating system, routing implementation, communications with a server, data binding, adjustability, size and activity of the community, quality of existing documentation, pos...

  17. Backbone decomposition for continuous-state branching processes with immigration

    Ren, A E Kyprianou Y-X

    2011-01-01

    In the spirit of Duqesne and Winkel (2007) and Berestycki et al. (2011) we show that supercritical continuous-state branching process with a general branching mechanism and general immigration mechanism is equal in law to a continuous-time Galton Watson process with immigration with Poissonian dressing. The result also characterises the limiting backbone decomposition which is predictable from the work on consistent growth of Galton-Watson trees with immigration in Cao and Winkel (2010).

  18. Variation of protein backbone amide resonance by electrostatic field

    Sharley, John N.

    2015-01-01

    Amide resonance is found to be sensitive to electrostatic field with component parallel or antiparallel the amide C-N bond. This effect is linear and without threshold in the biologically plausible electrostatic field range -0.005 to 0.005 au. Variation of amide resonance varies Resonance-Assisted Hydrogen Bonding such as occurs in the hydrogen bonded chains of backbone amides of protein secondary structures such as beta sheet and alpha helix, varying the stability of the secondary structure....

  19. Increasing protein production by directed vector backbone evolution

    Jakob, Felix; Lehmann, Christian; Martinez, Ronny; Schwaneberg, Ulrich

    2013-01-01

    Recombinant protein production in prokaryotic and eukaryotic organisms was a key enabling technology for the rapid development of industrial and molecular biotechnology. However, despite all progress the improvement of protein production is an ongoing challenge and of high importance for cost-effective enzyme production. With the epMEGAWHOP mutagenesis protocol for vector backbone optimization we report a novel directed evolution based approach to increase protein production levels by randoml...

  20. Internal protein dynamics on ps to μs timescales as studied by multi-frequency 15N solid-state NMR relaxation

    A comprehensive analysis of the dynamics of the SH3 domain of chicken alpha-spectrin is presented, based upon 15N T1 and on- and off-resonance T1ρ relaxation times obtained on deuterated samples with a partial back-exchange of labile protons under a variety of the experimental conditions, taking explicitly into account the dipolar order parameters calculated from 15N–1H dipole–dipole couplings. It is demonstrated that such a multi-frequency approach enables access to motional correlation times spanning about 6 orders of magnitude. We asses the validity of different motional models based upon orientation autocorrelation functions with a different number of motional components. We find that for many residues a “two components” model is not sufficient for a good description of the data and more complicated fitting models must be considered. We show that slow motions with correlation times on the order of 1–10 μs can be determined reliably in spite of rather low apparent amplitudes (below 1 %), and demonstrate that the distribution of the protein backbone mobility along the time scale axis is pronouncedly non-uniform and non-monotonic: two domains of fast (τ −10 s) and intermediate (10−9 s −7 s) motions are separated by a gap of one order of magnitude in time with almost no motions. For slower motions (τ > 10−6 s) we observe a sharp ∼1 order of magnitude decrease of the apparent motional amplitudes. Such a distribution obviously reflects different nature of backbone motions on different time scales, where the slow end may be attributed to weakly populated “excited states.” Surprisingly, our data reveal no clearly evident correlations between secondary structure of the protein and motional parameters. We also could not notice any unambiguous correlations between motions in different time scales along the protein backbone emphasizing the importance of the inter-residue interactions and the cooperative nature of protein dynamics

  1. Internal protein dynamics on ps to μs timescales as studied by multi-frequency {sup 15}N solid-state NMR relaxation

    Zinkevich, Tatiana [Martin-Luther-Universität Halle-Wittenberg, NMRGroup, Faculty of Natural Sciences II, Institut für Physik (Germany); Chevelkov, Veniamin [Max-Planck-Institut für Biophysikalische Chemie (Germany); Reif, Bernd [Technische Universität München, Department Chemie (Germany); Saalwächter, Kay; Krushelnitsky, Alexey, E-mail: krushelnitsky@physik.uni-halle.de [Martin-Luther-Universität Halle-Wittenberg, NMRGroup, Faculty of Natural Sciences II, Institut für Physik (Germany)

    2013-09-19

    A comprehensive analysis of the dynamics of the SH3 domain of chicken alpha-spectrin is presented, based upon {sup 15}N T{sub 1} and on- and off-resonance T{sub 1ρ} relaxation times obtained on deuterated samples with a partial back-exchange of labile protons under a variety of the experimental conditions, taking explicitly into account the dipolar order parameters calculated from {sup 15}N–{sup 1}H dipole–dipole couplings. It is demonstrated that such a multi-frequency approach enables access to motional correlation times spanning about 6 orders of magnitude. We asses the validity of different motional models based upon orientation autocorrelation functions with a different number of motional components. We find that for many residues a “two components” model is not sufficient for a good description of the data and more complicated fitting models must be considered. We show that slow motions with correlation times on the order of 1–10 μs can be determined reliably in spite of rather low apparent amplitudes (below 1 %), and demonstrate that the distribution of the protein backbone mobility along the time scale axis is pronouncedly non-uniform and non-monotonic: two domains of fast (τ < 10{sup −10} s) and intermediate (10{sup −9} s < τ < 10{sup −7} s) motions are separated by a gap of one order of magnitude in time with almost no motions. For slower motions (τ > 10{sup −6} s) we observe a sharp ∼1 order of magnitude decrease of the apparent motional amplitudes. Such a distribution obviously reflects different nature of backbone motions on different time scales, where the slow end may be attributed to weakly populated “excited states.” Surprisingly, our data reveal no clearly evident correlations between secondary structure of the protein and motional parameters. We also could not notice any unambiguous correlations between motions in different time scales along the protein backbone emphasizing the importance of the inter

  2. Isotopic variability of cave bears (δ15N, δ13C) across Europe during MIS 3

    Krajcarz, Magdalena; Pacher, Martina; Krajcarz, Maciej T.; Laughlan, Lana; Rabeder, Gernot; Sabol, Martin; Wojtal, Piotr; Bocherens, Hervé

    2016-01-01

    Collagen, the organic fraction of bone, records the isotopic parameters of consumed food for carbon (δ13C) and nitrogen (δ15N). This relationship of isotopic signature between diet and tissue is an important tool for the study of dietary preferences of modern and fossil animal species. Since the first information on the isotopic signature of cave bear was reported, numerous data from Europe have become available. The goal of this work is to track the geographical variation of cave bear collagen isotopic values in Europe during Marine Isotopic Stage 3 (about 60,000-25,000 yr BP). In this study the results of new δ13C and δ15N isotopic analyses of cave bear collagen from four Central-Eastern European sites are presented, as well as a review of all published isotopic data for cave bears of the same period. The main conclusion is a lack of geographical East-West pattern in the variations of δ13C and δ15N values of cave bear collagen. Moreover, no relationship was found between cave bear taxonomy and isotopic composition. The cave bears from Central-Eastern Europe exhibit δ13C and δ15N values near the average of the range of Central, Western and Southern European cave bears. Despite the fact that most cave bear sites follow an altitudinal gradient, separate groups of sites exhibit shift in absolute values of δ13C, what disturbs an altitude-related isotopic pattern. The most distinct groups are: high Alpine sites situated over 1500 m a.s.l. - in terms of δ13C; and two Romanian sites Peştera cu Oase and Urşilor - in case of δ15N. Although the cave bear isotopic signature is driven by altitude, the altitudinal adjustment of isotopic data is not enough to explain the isotopic dissimilarity of these cave bears. The unusually high δ15N signature of mentioned Romanian sites is an isolated case in Europe. Cave bears from relatively closely situated Central-Eastern European sites and other Romanian sites are more similar to Western European than to Romanian

  3. Fertilizer {sup 15}N balance in a coffee cropping system: a case study in Brazil

    Fenilli, Tatiele Anete Bergamo [Universidade Regional de Blumenau (URB), SC (Brazil). Dept. de Engenharia Florestal]. E-mail: tfenilli@furb.br; Reichardt, Klaus; Bacchi, Osny Oliveira Santos [Centro de Energia Nuclear na Agricultura (CENA/USP), Piracicaba, SP (Brazil). Lab. de Fisica do Solo]. E-mails: klaus@cena.usp.br; osny@cena.usp.br; Favarin, Jose Laercio [Escola Superior de Agricultura Luiz de Queiroz (ESALQ/USP), Piracicaba, SP (Brazil). Dept. de Producao Vegetal; Silva, Adriana Lucia [Centro de Tecnologia Canavieira (CTC), Piracicaba, SP (Brazil). Fazenda Santo Antonio]. E-mail: adriana.silva@ctc.com.br; Timm, Luis Carlos [Universidade Federal de Pelotas (UFPel), RS (Brazil). Dept. de Engenharia Rural]. E-mail: lcartimm@yahoo.com.br

    2008-07-15

    Knowledge about the fate of fertilizer nitrogen in agricultural systems is essential for the improvement of management practices in order to maximize nitrogen (N) recovery by the crop and reduce N losses from the system to a minimum. This study involves fertilizer management practices using the {sup 15}N isotope label applied in a single rate to determine the fertilizer-N balance in a particular soil-coffee-atmosphere system and to deepen the understanding of N plant dynamics. Five replicates consisting of plots of about 120 plants each were randomly defined within a 0.2 ha coffee plantation planted in 2001, in Piracicaba, SP, Brazil. Nine plants of each plot were separated in sub-plots for the {sup 15}N balance studies and treated with N rates of 280 and 350 kg ha-1 during 2003/2004 and 2004/ 2005, respectively, both of them as ammonium sulfate enriched to a {sup 15}N abundance of 2.072 atom %. Plant shoots were considered as separate parts: the orthotropic central branch, productive branches, leaves of productive branches, vegetative branches, leaves of vegetative branches and fruit. Litter, consisting of dead leaves accumulated below the plant canopy, was measured by the difference between leaves at harvest and at the beginning of the following flowering. Roots and soil were sampled down to a depth of 1.0 at intervals of 0.2 m. Samples from the isotopic sub-plots were used to evaluate total N and {sup 15}N, and plants outside sub-plots were used to evaluate dry matter. Volatilization losses of NH{sub 3} were estimated using special collectors. Leaching of fertilizer-N was estimated from deep drainage water fluxes and {sup 15}N concentrations of the soil solution at 1 m soil depth. At the end of the 2-year evaluation, the recovery of {sup 15}N applied as ammonium sulfate was 19.1 % in aerial plant parts, 9.4 % in the roots, 23.8 % in the litter, 26.3 % in the fruit and 12.6 % remaining in the 0-1.0 m soil profile. Annual leaching and volatilization losses were

  4. δ15N values of forage grasses and preliminary evaluation of their dinitrogen fixation potential for them

    There exist different δ15N values in shoots of different species and varieties of leguminosae grasses, showing that the potentialities of their dinitrogen fixation were apparently different. The δ15N values in shoots of some grasses tested were too low, and very close to δ15N value of atmospheric N2(0%). It is possible that they get N to meet the needs of their growth through some associative dinitrogen fixation processes. Further study should be done

  5. Does δ 15N in river food webs reflect the intensity and origin of N loads from the watershed?

    Stable nitrogen isotope ratios (δ 15N) were measured in invertebrates and fish collected from 82 river sites located in the Saint-Lawrence Lowlands in Quebec, Canada, to examine the relationship between aquatic biota δ 15N and anthropogenic nitrogen (N) loads. Mean δ 15N values of all three trophic levels examined (primary consumers, predatory invertebrates and invertebrate-feeding fish) were highly correlated with total anthropogenic N loads on the watershed (kg N km-2 year-1; r 2 > 0.61, p 2 > 0.62, p 2 > 0.45, p 2 > 0.29, p 15N and N loads originating from each of the three livestock species examined (bovines, pigs and poultry; p 15N (multiple r 2 = 0.67, p 15N values increasing slowly over a wide range of low levels of N loads, but increasing much faster as N loads grew larger. The three anthropogenic N sources examined were highly correlated with one another, preventing us from statistically isolating their respective effects on δ 15N. When these loads were expressed as a proportion of total N load, δ 15N of aquatic biota was still highly correlated with N from livestock and fertilizers, but not with N from human population. Overall, these results suggest that δ 15N values of aquatic consumers could be used as indicators of the intensity of anthropogenic N loading on watersheds, but not as tracers of the relative importance of individual N sources

  6. Study of the giant dipole resonances of 16O and 15N by means of radiative captures

    The giant dipole resonance in 16O and 15N is studied with reactions 14N(d,γ0)16O, 13C(3He,γ0)16O and 11B(α,γ0)15N. The same energy range is observed with transfert reactions as 12C(7Li,αγ)15N. A comparative study of radiative captures leading to 16O and 15N point out the importance of nsub(p)-nsub(t) configurations. Apparatus and experimental techniques developed are also described

  7. Study of organic N transformation in red soils by 15N tracer method

    YeQing-Fu; ZhangQin-Zheng; 等

    1997-01-01

    Uniformly 15N-labelled ryegrass was used to investigate NH4+-production,microbial transformation and humification of organic N in two types of red soils by incubating the soils amended with labelled material.The results showed that there was little significant difference in biomass N transformation in the tested solis between 15N tracer method and conventional method,but the amount of NH4++-N released form the ryegrass in the clayey soil than in the sandy soil at all sampling time .By 120d of incubation,humified N was less than 10% of the amount of the applied N in two types of red soils and the amount of residual N in the clayey red soil was obviously higher than that in the sandy red soil.

  8. The kinetics of the 15N/14N isotopic exchange between nitric oxide and nitric acid

    The rate of the 15N isotopic exchange between NO-NHO3 at high nitric acid concentration (2-10M) have been measured. The experimental data were obtained by contacting nitric oxide at atmospheric pressure with nitric acid solution labelled with 15N, in a glass contactor. The measurements were carried out in a glass vessel with magnetic stirrer maintaining always the same stirring rate (17 rot.s-1). The temperature was kept constant at 25 +-0.5 deg C. The reaction vessel was connected to a vacuum line and a purified nitric oxide source. The rate of the isotopic exchange and of the nitric oxide absorption in nitric acid were determined with a gas-burette in the simple apparatus described earlier. (T.G.)

  9. Nitrogen balance and 15N abundance in a long-term organic matter experiment

    In along-term field experiment on a clay loam soil at Uppsala, Sweden, changes of nitrogen contents and the natural abundance of 15N in the topsoils receiving various organic amendments at the rate of 2000 kg C ha-1 y-1 and different rates of nitrogen were studied. Cropping resulted in clearly lower N-losses from the topsoil (0-20 cm) compared to the bare fallow plots. Green manure, animal manure and sewage sludge increased the Nt-inventory significantly and 15N abundances were clearly affected by N-input differing in isotopic signature through the amendments. A N-balance and half-lives of the introduced nitrogen were calculated. Refs. 7 (author)

  10. Use of 15N and 13C for human nutrition research in Guatemala

    The use of stable non-radioactive isotopes have had an increased use in human nutrition research. Their application is particularly suited for those nutritional problems prevalent in the less-developed world. According to the contract, during the first year it is proposed to set up in Guatemala the necessary technology and to create the essential skills for the appropriate use and analysis of 15N. International and working standards have been analyzed using emission spectrometry (NOI 5E). Results from this work are reported to the IAEA. Clinical trials will be performed during the second half of the contract according to available resources. Changes in protein turn-over as measured by 15N-glycine in children with severe protein malnutrition will be assessed before and after recovery in order to determine metabolic adaptations. Results will be compared with normal controls. 21 refs, 2 tabs

  11. 1H, 13C and 15N NMR assignments of phenazopyridine derivatives.

    Burgueño-Tapia, Eleuterio; Mora-Pérez, Yolanda; Morales-Ríos, Martha S; Joseph-Nathan, Pedro

    2005-03-01

    Phenazopyridine hydrochloride (1), a drug in clinical use for many decades, and some derivatives were studied by one- and two-dimensional (1)H, (13)C and (15)N NMR methodology. The assignments, combined with DFT calculations, reveal that the preferred protonation site of the drug is the pyridine ring nitrogen atom. The chemoselective acetylation of phenazopyridine (2) and its influence on the polarization of the azo nitrogen atoms were evidenced by the (15)N NMR spectra. Molecular calculations of the phenazopyridines 2-4 show that the pyridine and phenyl groups are oriented in an antiperiplanar conformation with intramolecular hydrogen bonding between the N-b atom and the C-2 amino group preserving the E-azo stereochemistry. PMID:15625718

  12. Recovery of 15N-Urea under groundnut-sorghum sequence

    In 2 field experiments conducted at Agricultural Research Station, Tamil Nadu Agricultural University Farm, Bhavanisagar in red loamy soil (Typic Ustropept), the recovery of added 15N-urea was monitored under groundnut-sorghum cropping sequence. Fertilizer 15N was applied as urea at 5, 10 and 15 kg N/ha levels. The highest pod yield (2.18 t/ha) and haulm yield (13.19 t/ha) were recorded at 10 kg N ha-1 level. Out of 10 kg N applied, 51.86 per cent was recovered by the first crop of groundnut and found distributed as 43.13, 1.70 and 8.03 per cent in haulm, shell and kernel, respectively. The residual N recorded by the second crop of sorghum was only 0.63 per cent. (author). 4 refs., 4 tabs

  13. Fertilizer nitrogen recovery of rice : 15N field studies (a short review)

    Reliable quantitative estimates of fertilizer nitrogen recovery by rice are obtained in field investigations with 15N-labelled materials. Values obtained by conventional 'difference method' of comparing fertilized and unfertilized plots are typically larger than the actual values. Estimating the recovery of fertilizer nitrogen is not a goal in itself. Although it has been an essential component of limited number of 15N-field experiments conducted with rice so far; these provide little or no information about crop growth stages when fertilizer N is most efficiently utilized by rice plant. Recently, the path coefficient analysis has been used to analyse the effect of N uptake on the development of yield components and their contribution to grain yield. Nitrogen-15 fertilizers along with path coefficient analysis can prove particularly useful in comparing the efficiency of different N fertilizers and in the development of new and more efficient nitrogen sources and management practices. (author)

  14. Food webs of two intermittently open estuaries receiving 15N-enriched sewage effluent

    Hadwen, Wade L.; Arthington, Angela H.

    2007-01-01

    Carbon and nitrogen stable isotope signatures were used to assess the response of food webs to sewage effluent discharged into two small intermittently open estuaries in northern New South Wales, Australia. One of these systems, Tallows Creek, has a history of direct sewage inputs, whilst the other, Belongil Creek, receives wastewater via an extensive wetland treatment system. The food webs of both systems were driven by algal sources of carbon, reflecting high autotrophic productivity in response to the nutrients entering the system from sewage effluent. All aquatic biota collected from Tallows Creek had significantly enriched δ15N signatures relative to their conspecifics from Belongil Creek, indicating that sewage nitrogen had been assimilated and transferred throughout the Tallows Creek food web. These δ15N values were higher than those reported from studies in permanently open estuaries receiving sewage effluent. We suggest that these enriched signatures and the transfer of nitrogen throughout the entire food web reflect differences in hydrology and associated nitrogen cycling processes between permanently open and intermittently open estuaries. Although all organisms in Tallows Creek were generally 15N-enriched, isotopically light (less 15N-enriched) individuals of estuary perchlet ( Ambassis marianus) and sea mullet ( Mugil cephalus) were also collected. These individuals were most likely recent immigrants into Tallows Creek, as this system had only recently been opened to the ocean. This isotopic discrimination between resident (enriched) and immigrant (significantly less enriched) individuals can provide information on fish movement patterns and the role of heavily polluted intermittently open estuaries in supporting commercially and recreationally valuable estuarine species.

  15. Aqua ammonia 15 N obtaining and application with vainness for sugar-cane fertilization

    Nitrogen compounds marked with the isotope 15 N are continuously being used in agronomic studies and, when associated to the isotopic dilution technique, they constitute an important tool in clarifying the N cycle. At the Centro de Energia Nuclear na Agricultura (CENA/USP), it was obtained ( 15 NH4)2SO4 enhanced at 3,5% of 15 N atoms, by means of the ionic exchange chromatography technique, which made possible to produce aqua ammonia (15 NH3aq). Four repetitions were taken to the aqua ammonia production process to use the nitrogen compound in the field experiment. In each process 150g of ammonium sulfate enhanced at 3,5% of 15 N atoms was used, obtaining 31,0 ± 1,6 g of aqua ammonia on the average (80% yield), with the same enhancement. The incidence of isotopic dilution has not been observed during the procedure, what made the use of such methodology possible. After obtaining the aqua ammonia 15 N through this procedure, it was added to the vinasse (an equivalent to 50 m3 ha-1 ) in doses that corresponded to 70 kg ha-1 of N-NH3aq. The mixture was applied to the sugar-cane straw on the soil's surface, aimed to the crop's fertilization. The compound's isotopic composition was analyzed by means of a spectrometer of masses ANCA-SL Europe Scientific, while the total-N volatilized, by the micro-Kjeldahl. Method. In accordance to the low NH3 (6,4 ± 1,9 kg ha-1 ) volatilization results, it could be concluded that the application of vinasse and aqua ammonia mixture to the straw on the soil's surface was efficient, due to the vinasse's acid character, which allowed the NH3, in presence of the ion H+, to stay in the NH4+ form in solution. (author)

  16. δ15N in the turtle grass from the Mexican Caribbean

    Talavera-Saenz, A.; Sanchez, A.; Ortiz-Hernandez, M.

    2013-05-01

    Nutrient inputs associated with population growth threaten the integrity of coastal ecosystems. To assess the rapid increase in tourism, we compared the δ15N from Thalassia testudinum collected at sites with different levels of tourism development and population to detect the N inputs of wastewater discharge (WD) along the coast of Quintana Roo. The contributions of nitrogen enriched in 15N are directly related to the increase of WD inputs in areas of high tourism development (Nichupte Lagoon in Cancun, >3 million tourists per year from 2007 to 2011 and 0.7 million of resident population) and decreased towards Bahia Akumal and Tulum (>3 million tourists per year from 2007 to 2011 and 0.15 million of resident population). The δ15N from T. testudinum was significantly lower at Mahahual and Puerto Morelos (about 0.4 million tourists per year in 2007 to 2011 and 0.25 million of resident population) than other the sites. In areas of the lowest development and with tourist activity restricted and small population, such as the Yum Balam Reserve and Sian Ka'an Biosphere Reserve, the δ15N values were in much higher enrichment that Mahahual and Puerto Morelos. Therefore is suggested that Mahahual and Puerto Morelos may be used for baseline isotopic monitoring, over environmental pressure on the reef lagoon ecosystem, where tourist activities and population are growing very slow rate. The anthropogenic N input has the potential to impact, both environmentally and economically, the seagrass meadows and the coral reefs along the coast of Quintana Roo and the Caribbean.

  17. CHEMICALS

    Medical Service

    2002-01-01

    It is reminded that all persons who use chemicals must inform CERN's Chemistry Service (TIS-GS-GC) and the CERN Medical Service (TIS-ME). Information concerning their toxicity or other hazards as well as the necessary individual and collective protection measures will be provided by these two services. Users must be in possession of a material safety data sheet (MSDS) for each chemical used. These can be obtained by one of several means : the manufacturer of the chemical (legally obliged to supply an MSDS for each chemical delivered) ; CERN's Chemistry Service of the General Safety Group of TIS ; for chemicals and gases available in the CERN Stores the MSDS has been made available via EDH either in pdf format or else via a link to the supplier's web site. Training courses in chemical safety are available for registration via HR-TD. CERN Medical Service : TIS-ME :73186 or service.medical@cern.ch Chemistry Service : TIS-GS-GC : 78546

  18. 13N, 15N isotope and kinetic evidence against hyponitrite as an intermediate in denitrification

    13N- and 15N-labeling experiments were carried out with Paracoccus denitrificans, grown anaerobically on nitrate, to determine whether hyponitrite might be an obligatory intermediate in denitrification and a precursor of nitrous oxide. From experiments designed to trap [13N]- or [15N, 15N]hyponitrite by dilution into authentic hyponitrite it was calculated that the intracellular concentration of a presumptive hyponitrite pool must be less than 0.4 mm. In order for a pool of this size to turn over rapidly enough to handle the flux of nitrogen during denitrification, the spontaneous rate of hyponitrite dehydration must be enhanced by a factor of several thousand through enzyme catalysis. Cell extracts failed to catalyze this reaction under a variety of conditions. It is concluded that hyponitrite cannot be an intermediate in denitrification. In addition, the assimilation of inorganic nitrogen was studied in P. dentrificans using 13N as tracer. At low concentrations (-8 M) of labeled nitrate and nitrite 5 to 10% of the label was assimilated into non-volatile metabolites and 90 to 95% was reduced to N2. Similarly, with 15 mm [13N]nitrate, 5% of the label went into metabolites and 95% to N2. High pressure liquid chromatography analysis of the labeled metabolites indicated that the major pathway for assimilation of inorganic nitrogen in P. denitrificans under these conditions is through ammonia incorporation via the aspartase reaction

  19. Method of 15 N analysis by mass-spectrometry on ion implanter MPB-200

    The industrial implanter MPB-200 has been modified to a light-isotopes mass-spectrometer. Mass resolution has been improved by combination of the quadrupole focusing system and a collimator with additional scattering shielding. single beam method has been set up, in which mass-spectra are obtained by scanning magnetic field of the separator. A start-stop control system has been designed to operate automatically the magnet and registration system, from which signals are transferred to a XT/AT computer for saving and processing. The mass - resolution is satisfactory for analysis of light isotopes with mass number A less than 40. A testing measurement has been done with standard samples of natural and enriched 15 N isotope content. Obtained resolution and background condition allowed to achieve a good linear dependence of relative isotope ratio vs. real 15 N abundance in the range from natural (0.365%) to 5.0% with an accuracy of 3% (96% of reliability). Routine 15 N analysis may achieve the 5% - 10% accuracy by 7 - 10 minutes measurement for each sample. The new mass-spectroscopy system is applied in agricultural, biological and environmental studies. (author). 4 refs., 4 figs

  20. Determination of N2 -fixation ability of legume trees using the 15N method

    A sequence field experiment has been conducted for determining the capability of N2-fixation by several legume trees. The experiment was designed using a randomize design with 4 replicates. Each replicate was planted with 100 legume trees and 100 non legume trees. The isotope plot, where 15N was applied with 18 legume trees and 18 non legume trees. The planting distance was 1m x 1m. For the calculation of N2-fixation each legume and standard tree (Eucalypthus alba) was applied with 12.52g in the from of ammonium sulfate with 10.12% 15N. The 15N AS was applied in three splits 11 month earlier. Data obtained from this experiment showed that percentage of N derived from fixation (%N-dfF) of all legume trees was reasonable high. The legume trees used in this experiment were, Leucaena leucocephala, Acacia mangium, Caliandra tetragona, Flemengia congesta and Gliriciadia sepium with potential fixation from 62.31% to 90,68%. (author)

  1. Affordable uniform isotope labeling with 2H, 13C and 15N in insect cells

    For a wide range of proteins of high interest, the major obstacle for NMR studies is the lack of an affordable eukaryotic expression system for isotope labeling. Here, a simple and affordable protocol is presented to produce uniform labeled proteins in the most prevalent eukaryotic expression system for structural biology, namely Spodoptera frugiperda insect cells. Incorporation levels of 80 % can be achieved for 15N and 13C with yields comparable to expression in full media. For 2H,15N and 2H,13C,15N labeling, incorporation is only slightly lower with 75 and 73 %, respectively, and yields are typically twofold reduced. The media were optimized for isotope incorporation, reproducibility, simplicity and cost. High isotope incorporation levels for all labeling patterns are achieved by using labeled algal amino acid extracts and exploiting well-known biochemical pathways. The final formulation consists of just five commercially available components, at costs 12-fold lower than labeling media from vendors. The approach was applied to several cytosolic and secreted target proteins

  2. 13N,15N isotope and kinetic evidence against hyponitrite as an intermediate in dentrification.

    Hollocher, T C; Garber, E; Cooper, A J; Reiman, R E

    1980-06-10

    13N- and 15N-labeling experiments were carried out with Paracoccus denitrificans, grown anaerobically on nitrate, to determine whether hyponitrite might be an obligatory intermediate in denitrification and a precursor of nitrous oxide. From experiments designed to trap [13N]- or [15N,15N]hyponitrite by dilution into authentic hyponitrite it was calculated that the intracellular concentration of a presumptive hyponitrite pool must be less than 0.4 mM. In order for a pool of this size to turn over rapidly enough to handle the flux of nitrogen during dentrifucation, the spontaneous rate of hyponitrite dehydration must be enhanced by a factor of several thousand through enzyme catalysis. Cell extracts failed to catalyze this reaction under a variety of conditions. It is concluded that hyponitrite cannot be an intermediate in dentrification. In addition, the assimilation of inorganic nitrogen was studied in P. denitrificans using 13N as tracer. At low concentrations (less than 10(-8) M) of labeled nitrate and nitrite 5 to 10% of the label was assimilated into non-volatile metabolites and 90 to 95% was reduced to N2. Similarly, with 15 mM [13N]nitrate, 5% of the label went into metabolites and 95% to N2. High pressure liquid chromatography analysis of the labeled metabolites indicated that the major pathway for assimilation of inorganic nitrogen in P. denitrificans under these conditions is through ammonia incorporation via the aspartase reaction. PMID:7372623

  3. Recovery of 15N-labelled fertilizers applied to bromegrass on a thin black chernozem soil

    The availability of N fertilizers on established grass stands is a function of such processes as immobilization, gaseous loss, leaching and position of applied N. A field experiment was conducted on a Thin Black Chernozem soil at Crossfield, Alberta to determine the effect of source, time and method of application on the recovery of 15N-labelled fertilizers applied to smooth bromegrass (Bromus inermis Leyss.). The treatments included two sources of N [urea and ammonium nitrate (AN)], four application times (early autumn, late autumn, early spring and late spring) and two methods of placement (surface-broadcast and subsurface banding). In most cases the 15N recovery in soil did not differ much between urea and AN. However, when urea was surface-broadcast, there was, on average, 10.2% less 15N recovery in plants than AN. The N recovery for late spring > early spring > late autumn = early autumn. When urea was banded 4 cm deep into the soil, N recovery in plants increased significantly compared with its surface-broadcast application. However, this was not observed when the source of N was AN. Banding generally increased the amount of immobilized N present in the soil and N recovery. We concluded that the N recovery in plants and in plants plus soil was less for urea than for AN and was less with autumn broadcast N application than with spring broadcast application. (author). 23 refs., 3 tabs

  4. Fertilizer 15N balance and recovery of N from organic sources by rice in Typic Ustochrept

    To investigate the fertilizer-N balance and recovery of N from organics (as determined by A-value technique) by rice as affected by urea application alone or in combination with FYM or green manure, a field experiment was conducted in the khariff season if 1997 at IARI, New Delhi on a sandy loam soil (Typic Ustochrept). 15N-labelled urea was applied at 0.90 and 120 kg N ha-1 levels alone and in combination with either FYM or green manure in 2:1 or 1:1 ratios. Organic sources were incorporated seven days before transplanting whereas, urea was applied in three equal splits at 15 DAT, 28 DAT and 42 DAT. The residual 15N in soil was determined only in the surface soil layer (0-15 cm) of rice crop. The combined source helped in conserving more of urea-N in soil as residual (42-45%) than urea alone (23-27%) treatment due to the fact that the unaccounted fertilizer 15N was more in urea alone treatment (43-45%) than combined sources (12-15%) at both the levels. The efficiency of uptake of organic N by rice as determined through A-value technique was similar or better than urea-N at both the levels. (author)

  5. Plot-size for 15N-fertilizer recovery studies by tanzania-grass

    The understanding of the N dynamics in pasture ecosystems can be improved by studies using the 15N tracer technique. However, in these experiments it must be ensured that the lateral movement of the labeled fertilizer does not interfere with the results. In this study the plot-size requirements for 15N-fertilizer recovery experiments with irrigated Panicum maximum cv. Tanzania was determined. Three grazing intensities (light, moderate and intensive grazing) in the winter, spring and summer seasons were considered. A 1 m2 plot-size, with a grass tussock in the center, was adequate, irrespective of the grazing intensity or season of the year. Increasing the distance from the area fertilized with 15N negatively affected the N derived from fertilizer (Npfm) recovered in herbage.The lowest decline in Npfm values were observed for moderate and light grazing intensities. This fact might be explained by the vigorous growth characteristics of these plants. Increasing the grazing intensity decreased the tussock mass and, the smaller the tussock mass, the greater was the dependence on fertilizer nitrogen. (author)

  6. Magnetic shielding tensors of 13C and 15N in organic solids

    Magnetic shielding tensors delta have become accessible by Fourier transform NMR in high magnetic fields. Measurements were performed on 13C and 15N in powders and single crystals at frequencies of 61 and 32 MHz, respectively. Some of the general features of the shielding tensors have been established regarding the size of the anisotropy as well as the orientation of the principal axes system of delta relative to the molecule. This holds in particular for carbons involved sp2 bonds, where the direction of the largest shielding is found to be perpendicular to the sp2 plane. This can be understood theoretically showing that the shielding is dominated by the paramagnetic contribution. For 13C and 15N shielding tensors can be studied for isoelectronic systems, e.g. benzoation and nitrobenzene. Comparison of the shielding anisotropies Δdelta for a number of isoelectronic pairs shows that Δdelta generally seems to be substantially larger for 15N. The powder spectra are affected in a characteristic way by molecular motions in the solid. By analysis of the lineshapes observed it is therefore possible to get reliable information about molecular reorientation in solids. As an example the motion of the P4 tetrahedra in solid white phosphorus is discussed. (orig.)

  7. Incorporation of 15N into subcellular fractions and soluble proteins in rice seedlings

    15N incorporation into the subcellular and protein fractions of rice seedlings was investigated, when (15NH4)2SO4 was fed through culture solution, and the following was found. (1) Optical emission spectroscopic method is very useful for the 15N analysis of small amount of protein as much as separated by Sephadex G-200. (2) In the developed leaves, where nitrogen was balanced by continuous influx and efflux, 6 to 9 percent of total nitrogen was exchanged in a day by newly absorbed nitrogen, and the absorbed nitrogen was incorporated into chloroplast, 30,000 x g precipitate and soluble protein fractions by almost equal rates. (3) In the developing leaf, where the amount of nitrogen was increasing, newly absorbed and redistributed nitrogen almost equally contributed to the increase of total and protein nitrogen. (4) The speed of 15N incorporation into Fraction 1 Protein was the same in the developing leaf and slow in the developed leaves in comparison with other soluble proteins. (author)

  8. Behavior of 15N-labelled amino acids in germinated corn

    By investigating the rise and fall of 15N-labelled amino acids in germinated corns, the behavior of amino radicals in free amino acids, the influence of the hydrolysis products of stored proteins on free amino acids and the change from heterotrophy to autotrophy of seeds were clarified. The amount of amino acid production depending on external nitrogen was very small in the early period of germination. 15N incorporation into proline was not observed in the early period of germination, which suggested that the proline may be nitrogen-storing source. Most of the amino-state nitrogen of asparagine accumulated at the time of germination was internal nitrogen, and this fact suggested that aspartic acid serve as the acceptor of ammonia produced in the early stage of germination. 15N content increased significantly on 9 th day after germination, and decreased on 12 th day. These facts prove that there are always active decomposition and production of protein in plant body. (Kobatake, H.)

  9. Cucumber N need under protected cultivation using 15N-labelled urea

    To measure the N uptake and utilisation by plants, labelled 15N has been used. In this paper 15N-labelled urea was applied to cucumber under protected cultivation for two seasons, 1996/97 and 1997/98. Four levels of urea-N (0, 200, 400 and 600 kg N ha -1) were used in a complete randomised block design with 8 replicates. The experiment was conducted in the UAE at the Hurnraniyah Agriculture Research Station (HARS) in collaboration with the International Atomic Energy Agency (IAEA). From the obtained results it was clear that the average optimal fertiliser rate was 200 kg N ha -1. The N yield in the plant dry matter (fruits, shoots and roots) was 6.13 g N/plant under the specific experimental conditions (the area per plant was 1.23 m2 ). Using 15 N, it was found that the fertiliser N yield obtained for the same plant parts was 1.82 g N/plant. (author)

  10. 1H, 13C and 15N NMR spectral and X-ray structural studies of 2-arylsulfonylamino-5-chlorobenzophenones

    Six 2-(4-R-phenylsulfonylamino)-5-chlorobenzophenones were prepared and their 1H, 13C and 15N NMR spectra recorded and assigned. The dependence between the chemical shift of the amide proton and Hammett σ substituent constants is of the V type. Substituent effect on the chemical shift of the amide nitrogen atom was found insignificant. X-ray analysis shows that the terminal benzene rings in 2-(4-nitro-phenylsulfonylamino)-5-chlorobenzophenones are located close to each other. They are not, however, parallel, dihedral angle between them being equal to 10.86 deg (MP2/6-31G**//HF/6-31G** ab initio calculations show this to be 20.44 deg). This shows that the mutual orientation of two benzene rings in the molecule of this compound is caused by the π-π stacking. It is additionally reinforced by the intramolecular NH...O=C hydrogen bond. Except the dihedral angle between the benzene rings, X-ray determined structure of 2-(4-nitro-phenylsulfonylamino)-5-chlorobenzophenones is very similar to this optimized by the ab initio calculations. (author)

  11. Control of polymer-packing orientation in thin films through synthetic tailoring of backbone coplanarity

    Chen, Mark S.

    2013-10-22

    Controlling solid-state order of π-conjugated polymers through macromolecular design is essential for achieving high electronic device performance; yet, it remains a challenge, especially with respect to polymer-packing orientation. Our work investigates the influence of backbone coplanarity on a polymer\\'s preference to pack face-on or edge-on relative to the substrate. Isoindigo-based polymers were synthesized with increasing planarity by systematically substituting thiophenes for phenyl rings in the acceptor comonomer. This increasing backbone coplanarity, supported by density functional theory (DFT) calculations of representative trimers, leads to the narrowing of polymer band gaps as characterized by ultraviolet-visible-near infrared (UV-vis-NIR) spectroscopy and cyclic voltammetry. Among the polymers studied, regiosymmetric II and TII polymers exhibited the highest hole mobilities in organic field-effect transistors (OFETs), while in organic photovoltaics (OPVs), TBII polymers that display intermediate levels of planarity provided the highest power conversion efficiencies. Upon thin-film analysis by atomic force microscropy (AFM) and grazing-incidence X-ray diffraction (GIXD), we discovered that polymer-packing orientation could be controlled by tuning polymer planarity and solubility. Highly soluble, planar polymers favor face-on orientation in thin films while the less soluble, nonplanar polymers favor an edge-on orientation. This study advances our fundamental understanding of how polymer structure influences nanostructural order and reveals a new synthetic strategy for the design of semiconducting materials with rationally engineered solid-state properties. © 2013 American Chemical Society.

  12. Influence of Backbone Fluorination in Regioregular Poly(3-alkyl-4-fluoro)thiophenes

    Fei, Zhuping

    2015-06-03

    © 2015 American Chemical Society. We report two strategies toward the synthesis of 3-alkyl-4-fluorothiophenes containing straight (hexyl and octyl) and branched (2-ethylhexyl) alkyl groups. We demonstrate that treatment of the dibrominated monomer with 1 equiv of alkyl Grignard reagent leads to the formation of a single regioisomer as a result of the pronounced directing effect of the fluorine group. Polymerization of the resulting species affords highly regioregular poly(3-alkyl-4-fluoro)thiophenes. Comparison of their properties to those of the analogous non-fluorinated polymers shows that backbone fluorination leads to an increase in the polymer ionization potential without a significant change in optical band gap. Fluorination also results in an enhanced tendency to aggregate in solution, which is ascribed to a more co-planar backbone on the basis of Raman and DFT calculations. Average charge carrier mobilities in field-effect transistors are found to increase by up to a factor of 5 for the fluorinated polymers.

  13. Effect of organic matter application on the fate of 15N-labeled ammonium fertilizer in an upland soil

    The effect of the application of organic matter on the fate of 15N-labeled ammonium was investigated in a field. The organic materials incorporated into the experimental plots consisted of wheat straw, rape, pig compost, cow compost, plant manure. In May 2000, 10 g N m-2 of 15N-labeled ammonium was applied to the field together with the organic materials, and maize and winter wheat were consecutively cultivated. The recovery of applied 15N in soils and plants was determined after the harvest of each crop. Although only about 10% of the applied 15N-labeled fertilizer remained in the 0-30 cm layer of the Control Plot and the Plant Manure Plot, more than 25% of the applied 15N remained in the Pig Compost Plot. Amount and proportion of the immobilized 15N to those of total N or microbial biomass N in soils were determined for the topsoil samples (0-10 cm layer). The amounts of both microbial biomass N and total immobilized 15N in soil were highest in the Pig Compost Plot. Although the amount of microbial biomass N was comparable to the amount of immobilized 15N-labeled fertilizer in soil, the amounts of 15N-labeled fertilizer contained in the microbial biomass accounted for less than 10 % of the amount of total immobilized 15N in soil. The ratio of the amount of 15N-labeled fertilizer contained in biomass N to the total amount of biomass N was one order to magnitude higher than the ratio of the amount of immobilized 15N-labeled fertilizer to the amount of total N in soil. No conspicuous changes in the amount of immobilized 15N in soil were observed during the cultivation of winter wheat except for the Pig Compost Plot. No significant correlation was recognized between the amount of 15N-labeled fertilizer contained in microbial biomass before wheat cultivation and that of 15N-labeled fertilizer absorbed by wheat, indicating that microbial N immobilized during the growth period of the former crop (maize) was not a significant source of N for the latter crop (wheat

  14. Unusually negative nitrogen isotopic compositions (δ15N of mangroves and lichens in an oligotrophic, microbially-influenced ecosystem

    I. Romero

    2008-12-01

    Full Text Available Extremes in δ15N values in mangrove tissues and lichens (range =+4 to −22‰ were measured from a mangrove forest ecosystem located on Twin Cays, offshore islands in Belize, Central America. The N isotopic compositions and concentrations of NH4+/NH3 in porewater, rainwater, and atmospheric ammonia, and the δ15N of lichens, mangrove leaves, roots, stems, and wood were examined to study the biogeochemical processes important for establishing these unusual N isotopic ratios. Dwarfed Rhizophora mangle trees had the most negative δ15N, whereas fringing Rhizophora trees, the most positive δ15N values. Porewater ammonium concentrations had little relationship to N isotopic fractionation in mangrove tissues. In dwarfed mangroves, the δ15N of fine and coarse roots were 6–9‰ more positive than leaf tissue from the same tree, indicating different sources of N for root and leaf tissues. When P was added to dwarfed mangrove trees without added N, δ15N increased within one year from −12‰ to −2‰, approaching the δ15N of porewater ammonium (δ15N=+4‰. Isotopically depleted ammonia in the atmosphere (δ15N=−19‰ and in rainwater (δ15N=−10‰ were found on Twin Cays. We propose that foliar uptake of these atmospheric sources by P-stressed, dwarfed mangrove trees and lichens can explain their very negative δ15N values. In environments where P is limiting for growth, uptake of atmospheric N by Rhizophora mangle may be an important adaptive strategy.

  15. Nitrogen dynamics in legume-cereal rotations - The role of 15N

    Full text:15N-labelled fertilizers have been widely used to estimate N fertilizer recovery by cereal crops, residual fertilizer-derived N in the soil after harvest and losses from the soil-plant system by mass balance. Similarly 15N isotope dilution has been widely used to estimate the proportion of above-ground legume N derived from biological N2 fixation (Chalk and Ladha 1999). Both of these techniques provide information that cannot be obtained by non-isotopic or N difference methodologies. For example, the 15N dilution method enables the effect of any variable on legume symbiotic dependence to be differentiated from its effect on legume growth. i.e. it is a yield-independent methodology (Chalk 2000). 15N methodologies also have significant yet under utilized roles to play in estimating the fluxes of biologically fixed N in legume-cereal intercrops and rotations and hence in the prediction of system sustainability (Chalk 1996, 1998). The role of legumes in the overall N economies of cropping systems has long been the subject of conjecture and debate. Agronomically significant N yield responses of cereals following grain legumes compared with cereal monoculture are frequently measured. The positive N response of the cereal has been attributed to the transfer of biologically-fixed N, to N-sparing under the antecedent legume, and to less immobilization of nitrate during the decomposition of legume residues. Methods for estimating the transfer of biologically-fixed N in rotations, and for separating the N benefit into fixed N and non-fixed N components are reviewed. Available data indicate that both sources of N contribute to the N benefit. The role of grain legumes in the gain or drain of soil N is evaluated by considering the balance between symbiotic dependence and N harvest index, as well as long-term changes in total soil N. Several 15N-based techniques for direct estimation of inputs of biologically-fixed N to the soil N pool are reviewed. The contribution of

  16. Fluorous Peptide Nucleic Acids: PNA Analogues with Fluorine in Backbone (γ-CF2-apg-PNA) Enhance Cellular Uptake.

    Ellipilli, Satheesh; Ganesh, Krishna N

    2015-09-18

    Fluorous PNA analogues possessing fluorine as inherent part of aminopropylglycine (apg) backbone (γ-CF2-apg PNA) have been synthesized and evaluated for biophysical and cell penetrating properties. These form duplexes of higher thermal stability with cRNA than cDNA, although destabilized compared to duplexes of standard aeg-PNA. Cellular uptake of the fluorinated γ-CF2-apg PNAs in NIH 3T3 and HeLa cells was 2-3-fold higher compared to that of nonfluorinated apg PNA, with NIH 3T3 cells showing better permeability compared to HeLa cells. The backbone fluorinated PNAs, which are first in this class, when combined with other chemical modifications may have potential for future PNA-based antisense agents. PMID:26322827

  17. A new default restraint library for the protein backbone in Phenix: a conformation-dependent geometry goes mainstream

    Moriarty, Nigel W.; Tronrud, Dale E.; Adams, Paul D.; Karplus, P. Andrew

    2016-01-01

    Chemical restraints are a fundamental part of crystallographic protein structure refinement. In response to mounting evidence that conventional restraints have shortcomings, it has previously been documented that using backbone restraints that depend on the protein backbone conformation helps to address these shortcomings and improves the performance of refinements [Moriarty et al. (2014 ▸), FEBS J. 281, 4061–4071]. It is important that these improvements be made available to all in the protein crystallography community. Toward this end, a change in the default geometry library used by Phenix is described here. Tests are presented showing that this change will not generate increased numbers of outliers during validation, or deposition in the Protein Data Bank, during the transition period in which some validation tools still use the conventional restraint libraries. PMID:26894545

  18. Dynamics of the amino acid and protein metabolism of laying hens after the application of 15N-labelled wheat protein. 8

    Over 4 days 12 colostomized laying hens received, together with the ration, 36 g wheat with 14.37 atom-% 15N excess (15N'). The basic amino acids were nearly equally labelled. Three animals each were butchered after 12 h, 36 h, 60 h, and 108 h, resp., after the last 15N' application. Emission spectrometric determination of 15N' in liver and in amino acids was carried out. In addition, atom-% 15N' was determined in free amino acids and peptides. The labelling in the liver 12 h after the last 15N' application amounted to 1.75 atom-% 15N' and decreased after 108 h to 0.81 atom-% 15N'. The average TCA precipitable 15N' quota in the total 15N' amounted to 81.4% and was nearly identical at all four measuring points. The arginine 15N' amount in the liver was twice as high as that of lysine 15N'. In dependence on the period after the last 15N' application the decrease in the labelling of free arginine is considerable in comparison to free lysine. At the first measuring point (12 h) it was 1.69 atom-% 15N' and at the last one (108 h) 0.57 atom-% 15N'. Based on the results of 15N' labelling of peptides in the liver further, more detailed experiments for studies of peptide metabolism in the liver should be carried out. (author)

  19. Rapid mass spectrometric analysis of 15N-Leu incorporation fidelity during preparation of specifically labeled NMR samples

    Truhlar, Stephanie M E; Cervantes, Carla F; Torpey, Justin W;

    2008-01-01

    analyzing the isotopic abundance of the peptides in the mass spectra using the program DEX. This analysis determined that expression with a 10-fold excess of unlabeled amino acids relative to the (15)N-amino acid prevents the scrambling of the (15)N label that is observed when equimolar amounts are used......Advances in NMR spectroscopy have enabled the study of larger proteins that typically have significant overlap in their spectra. Specific (15)N-amino acid incorporation is a powerful tool for reducing spectral overlap and attaining reliable sequential assignments. However, scrambling of the label...... during protein expression is a common problem. We describe a rapid method to evaluate the fidelity of specific (15)N-amino acid incorporation. The selectively labeled protein is proteolyzed, and the resulting peptides are analyzed using MALDI mass spectrometry. The (15)N incorporation is determined by...

  20. Synthesis of tetrazole-13C and 1,2,4-triazole-1,2-15N2

    We report here the syntheses of tetrazole-13C and 1,2,4-triazole-1,2-15N2 by simple, one-step procedures using common, commercially available, isotopically-labeled starting materials. Tetrazole-13C is conveniently prepared from K13CN and NaN3 in 70% yield, almost twice the best reported yield for (unlabeled) tetrazole by similar synthetic methods. 1,2,4-triazole-1,2-15N2 was synthesized in 35% yield from hydrazine-15N2 sulphate and 1,3,5-triazine. From 15N-NMR we determined that 15N was specifically incorporated into the 1 and 2 positions of the triazole ring. (author)

  1. Sequential diffusion of ammonium and nitrate from soil extracts to a polytetrafluoroethylene trap for 15N determination

    A novel diffusion method was used for preparation of NH4+- and NO3--N samples from soil extracts for 15N determination. Ammonium, and nitrate following reduction to ammonia, are allowed to diffuse to an acid-wetted glass filter enclosed in polytetrafluoroethylene tape. The method was evaluated with simulated soil extracts obtained using 50 ml of 2 M potassium chloride solution containing 130 μg of NH4=-N (2.3 atom% 15N) and 120 μg of NO3--N (natural 15N abundance). No cross-over in the 15N abundances of NH4+-N and NO3--N was observed, indicating a quantitative diffusion process (72 h, 25 deg C). Owing to the presence of inorganic nitrogen impurities in the potassium chloride, the 15N enrichments should be corrected for the blank nitrogen content. (author). 8 refs.; 1 tab

  2. A 15N-poor isotopic composition for the solar system as shown by Genesis solar wind samples.

    Marty, B; Chaussidon, M; Wiens, R C; Jurewicz, A J G; Burnett, D S

    2011-06-24

    The Genesis mission sampled solar wind ions to document the elemental and isotopic compositions of the Sun and, by inference, of the protosolar nebula. Nitrogen was a key target element because the extent and origin of its isotopic variations in solar system materials remain unknown. Isotopic analysis of a Genesis Solar Wind Concentrator target material shows that implanted solar wind nitrogen has a (15)N/(14)N ratio of 2.18 ± 0.02 × 10(-3) (that is, ≈40% poorer in (15)N relative to terrestrial atmosphere). The (15)N/(14)N ratio of the protosolar nebula was 2.27 ± 0.03 × 10(-3), which is the lowest (15)N/(14)N ratio known for solar system objects. This result demonstrates the extreme nitrogen isotopic heterogeneity of the nascent solar system and accounts for the (15)N-depleted components observed in solar system reservoirs. PMID:21700869

  3. Design of an IPTV Multicast System for Internet Backbone Networks

    Gilbert, D.; Szymanski, T. H.

    2010-01-01

    The design of an IPTV multicast system for the Internet backbone network is presented and explored through extensive simulations. In the proposed system, a resource reservation algorithm such as RSVP, IntServ, or DiffServ is used to reserve resources (i.e., bandwidth and buffer space) in each router in an IP multicast tree. Each router uses an Input-Queued, Output-Queued, or Crosspoint-Queued switch architecture with unity speedup. A recently proposed Recursive Fair Stochastic Matrix Decompos...

  4. Performance of Flow-Aware Networking in LTE backbone

    Sniady, Aleksander; Soler, José

    2012-01-01

    According to traffic predictions, the growth in data networks usage will be increasing in the coming years, what will be especially visible in the mobile access networks. This brings new challenges in terms of traffic differentiation and network resource sharing, which need to be faced by wireless...... technologies, such as Long Term Evolution (LTE). This paper proposes usage of a modified Flow Aware Networking (FAN) technique for enhancing Quality of Service (QoS) in the all-IP transport networks underlying LTE backbone. The results obtained with OPNET Modeler show that FAN, in spite of being relatively...

  5. Synthesis of Polynucleotide Analogs Containing a Polyvinyl Alcohol Backbone

    Per Carlsen

    2008-03-01

    Full Text Available Water soluble homo-base polynucleotide analogues were synthesized in whichpolyvinyl alcohol and partially phosphonated polyvinyl alcohol constituted the backbones,onto which were grafted uracil or adenine via 1,3-dioxane spacers formed by acetalformation with the 1,3-diol moieties in PVA. The resulting adenine-PVA polynucleotideanalogs exhibited hyperchromic effects, which was not the case for the correspondinguracil compounds. Mixtures of the adenine- and aracil PVA-phosphate polynucleotideanalogs in solutions exhibited characteristic S-shaped UV-absorbance vs temperature andmelting curves with melting points at approximately 40 oC.

  6. Application of Multicast-based Video Conference on CERNET Backbone

    2002-01-01

    Multicast-based video conference is a representative application in advanced network. In multi-point video conference using multicast can get better efficiency facilitated by inner-group broadcast mechanism. In the application, the multicast-based network resources assignment, management and security should be considered together. This paper presents a framework model of multicast-based video conferencing application with three layers. And a practical multicast-based video conferencing is implemented in CERNET(China Education and Research Network) backbone. The practice is valuable for the development of multicast-based video conferencing application in China.

  7. Increased Diels-Alderase activity through backbone remodeling guided by Foldit players.

    Eiben, Christopher B; Siegel, Justin B; Bale, Jacob B; Cooper, Seth; Khatib, Firas; Shen, Betty W; Players, Foldit; Stoddard, Barry L; Popovic, Zoran; Baker, David

    2012-02-01

    Computational enzyme design holds promise for the production of renewable fuels, drugs and chemicals. De novo enzyme design has generated catalysts for several reactions, but with lower catalytic efficiencies than naturally occurring enzymes. Here we report the use of game-driven crowdsourcing to enhance the activity of a computationally designed enzyme through the functional remodeling of its structure. Players of the online game Foldit were challenged to remodel the backbone of a computationally designed bimolecular Diels-Alderase to enable additional interactions with substrates. Several iterations of design and characterization generated a 24-residue helix-turn-helix motif, including a 13-residue insertion, that increased enzyme activity >18-fold. X-ray crystallography showed that the large insertion adopts a helix-turn-helix structure positioned as in the Foldit model. These results demonstrate that human creativity can extend beyond the macroscopic challenges encountered in everyday life to molecular-scale design problems. PMID:22267011

  8. Inhibition of alanine racemase by alanine phosphonate: detection of an imine linkage to pyridoxal 5'-phosphate in the enzyme-inhibitor complex by solid-state 15N nuclear magnetic resonance

    Inhibition of alanine racemase from the Gram-positive bacterium Bacillus stearothermophilus by (1-aminoethyl)phosphonic acid (Ala-P) proceeds via a two-step reaction pathway in which reactivation occurs very slowly. In order to determine the mechanism of inhibition, the authors have recorded low-temperature, solid-state 15N NMR spectra from microcrystals of the [15N]Ala-P-enzyme complex, together with spectra of a series of model compounds that provide the requisite database for the interpretation of the 15N chemical shifts. Proton-decoupled spectra of the microcrystals exhibit a line at ∼ 150 ppm, which conclusively demonstrates the presence of a protonated Ala-P-PLP aldimine and thus clarifies the structure of the enzyme-inhibitor complex. They also report the pH dependence of Ala-P binding to alanine racemase

  9. The use of 15N in following organic matter turnover, with specific reference to rotation systems

    The results of this experiment indicate that the use of the technique described, (based on the degree of 15N-labelling of an N2 fixer and a non-fixer), may be of value in assessing N2 fixation in the field by legumes, but it is apparent that there are some problems to be overcome. Analyses of the whole plant are necessary, since the proportions of legume N due to N2 fixation vary with the plant part. The extent to which legumes take up available N from the soil obviously will vary with soil profile and plant properties; and they will be affected by sward density and competition from other plants. These latter factors will increase the difficulty of using this method for assessing N2 fixation by legumes in grazed pastures, but probably they would not be big problems when applying the method to grain legume crops. It is important that, in comparing the extent of labelling of the N of fixing and non-fixing plants, both types of plants should have access to soil inorganic-N of the same enrichment. This will be difficult to achieve under field conditions. However soils which contain relatively stable 15N-labelled organic residues may yield NO3-N of tolerably constant enrichments. An experiment is in progress at Avon in which soils, amended 15 months previously with 15N-labelled legume residues and then cropped to wheat, will remain in situ and will be sown with fixing and non-fixing plants during the 1980 and 1981 seasons. These soils may prove to be suitable for measuring N2 fixation in the field. (orig./MG)

  10. Banding urea and lignosulfonate in corn (Zea mays L.) production and 15N recovery

    The use of urea in corn (Zea mays L.) production is common. Under current N fertilizer recommendations for corn, urea may have adverse effects on corn growth when applied in a band. The effects of ammonium lignosulfonate (LS) on corn growth and on N uptake from the banded application of urea and diammonium phosphate (DAP) mixtures were investigated on two soils from eastern Quebec. Field experiments were initiated in the first week of May 1991 on an Ormstown silty clay and a Ste. Rosalie clay soils (fine, mixed, nonacid, mesic Typic Humaquepts). Treatments were two rates of urea (30 and 90 kg urea-N ha-1) in a combination with DAP (14kg N ha 1), with or without banded fertilizer solutions of LS (8 kg N ha-1) applied at planting 5 cm to the side and 3 cm below the seed. A no treatment control was included. The low rate of urea compared with the unfertilized plots. When compared with the unfertilized treatment, the high rate of urea and DAP (no LS added) caused 10% increase in grain yield. However, addition of LS to the high rate of urea and DAP increase grain yield by band 20%. In general, LS significantly increased corn N uptake from urea on both soils. Separate 15N field experiments were initiated in June 1991. Mean recovery of 15N ranged from 17.8% to 30.9% of the applied labelled urea. The rate of urea-N banded had no significant effect on immobilization, but LS resulted in significantly less 15N immobilized. These observations suggest that LS can reduce the biological immobilization of urea-N and increase the efficiency of urea fertilizer by reducing the negative effects of banding high levels of urea, while attaining benefits of band placement. (author). 29 refs., 6 tabs

  11. Nitrogen (15N) accumulation in corn grains as affected by source of nitrogen in red latosol

    Nitrogen is the most absorbed mineral nutrient by corn crop and most affects grains yield. It is the unique nutrient absorbed by plants as cation (NH4+) or anion (NO3-). The objectives of this work were to investigate the N accumulation by corn grains applied to the soil as NH4+ or NO3- in the ammonium nitrate form compared to amidic form of the urea, labeled with 15N; to determine the corn growth stage with highest fertilizer N utilization by the grains, and to quantify soil nitrogen exported by corn grains. The study was carried out in the Experimental Station of the Regional Pole of the Sao Paulo Northwestern Agribusiness Development (APTA), in Votuporanga, State of Sao Paulo, Brazil, in a Red Latosol. The experimental design was completely randomized blocks, with 13 treatments and four replications, disposed in factorial outline 6x2 + 1 (control, without N application). A nitrogen rate equivalent to 120 kg N ha-1 as urea-15N or as ammonium nitrate, labeled in the cation NH4+ (15NH4+NO3-) or in the anion NO3- (NH4+15N+O3- ), was applied in six fractions of 20 kg N ha-1 each, in different microplots, from seeding to the growth stage 7 (pasty grains). The forms of nitrogen, NH4+-N and NO3--N, were accumulated equitably by corn grains. The corn grains accumulated more N from urea than from ammonium nitrate. The N applied to corn crop at eight expanded leaves stage promoted largest accumulation of this nutrient in the grains. (author)

  12. Distillation and Microdiffusion Modifications for total Nh4f Quantification and 15N Recovery

    Gaius D. Eudoxie

    2008-01-01

    Full Text Available Problem statement: Applying 15N techniques to accurately determine the fate of fixed ammonium (NH4f in the strongly and weakly held pools require modifications to existing methodologies. Modifications are necessary for measurement of total NH4f in soils by direct digestion with 5 M HF: 1 M HCl, excluding alkali pretreatment, followed by distillation and quantification of NH4. Quantification by distillation was used as a precursor to optimize microdiffusion protocols for continuous flow-isotope ratio mass spectrometry (CF-IRMS. This paper reports on the modifications applied to these procedures since the direct 5 M HF: 1 M HCl digestion of soil samples may also dissolve some organic N fractions. Approach: Distillation followed by 15N microdiffusion trials were conducted on soil digests amended with rice husks, manure, compost or glycine, using different molarities (2, 5, and 10 M and volumes (5, 10, 15, 25, 32.5, and 40 mL of KOH. Results: The distillation study identified 32.5 mL of 2 M KOH to be the optimum volume and molarity of KOH that must be combined with 10-mL aliquots of direct 5 M HF: 1 M HCl digests of each of seven soils to ensure that only NH4 in the digest is recovered and none of the organic N is hydrolyzed during the process. Results also showed that a minimum incubation time of 192 h was needed to trap approximately 100 µg 15N on the disks for subsequent accurate analysis by CF-IRMS, with minimal recovery of organic N. Conclusions/Recommendations: These findings support the use of a direct-digestion/distillation method to quantify total NH4f and thereby provide opportunity to distinguish between strongly and weakly held NH4f in soils.

  13. Nitrogen fixation by free-living organisms in rice soils. Studies with 15N

    Heterotrophic nitrogen fixation as influenced by water regime, organic matter, combined nitrogen and pesticides was investigated in several Indian rice soils by means of the 15N2 tracer technique. Soil submergence accelerated nitrogen fixation. Addition of cellulose to both non-flooded and flooded soils enhanced nitrogen fixation. Under submerged conditions, addition of sucrose, glucose and malate in that order stimulated nitrogen fixation in alluvial soil, while only sucrose enhanced nitrogen fixation in laterite soil. Nitrogen fixation in flooded alluvial and laterite soils decreased with increasing concentration of combined nitrogen. Nitrogen fixation was appreciable in acid sulphate and saline soils under both flooded and non-flooded conditions, despite high salinity and acidity. Application of certain pesticides at rates equivalent to recommended field level greatly influenced nitrogen fixation in flooded rice soils. Additions of benomyl (carbamate fungicide) and carbofuran (methyl carbamate insecticide) to alluvial and laterite soils resulted in significant stimulation of nitrogen fixation. Gamma-BHC stimulated nitrogen fixation only in alluvial soil, with considerable inhibition in a laterite soil. Nitrogen fixation by Azospirillum lipoferum was investigated by 15N2. Large variations in 15N2 incorporation by A. lipoferum isolated from the roots of several rice cultivars was observed. Specific lines of rice harbouring A. lipoferum with high nitrogenase activity might be selected. Nitrogen fixed by heterotrophic organisms in a complex system such as soil could not be evaluated precisely. Indigenous nitrogen fixation in a flooded soil would be in the range of 5-10 kg N/ha, increasable 3 to 4-fold by appropriate fertilizers and cultural practices

  14. Preparation of sup(15)N-uran from KNO sub(3)-sup(15)N and (NH4)sub(2)SOsub(4)-sup(15)N with independent isotopic labelling of the sources N-NOsub(3), N-NHsub(4) and N-NHsub(2)

    Processes to obtain ammonium nitrate sup(15)N-labeled in the nitric component starting from potassium sup(15)N-nitrate and using cationic exchange technique, and the same compound labeled in the ammonium component, through distillation of ammonia-sup(15)N followed by stoichiometric reaction with HNO sub(3) solution are described. With the ammonium nitrate thus obtained, and labeled either in the NH sub(4) or No sub(3) component plus urea-sup(15)N, it is possible to prepare the fluid fertilizer URAN labeled independently in any of its nitrogen components. The sup(15)N labeled URAN can then be used as a tracer in fertilizer studies. (author)

  15. Mineralization of 15N-labelled sheep manure in soils of different texture and water contents

    I. K. Thomsen; Schjønning, P.; B. T. Christensen

    2003-01-01

    In order to investigate the effect of soil moisture and texture on C and N mineralization of applied organic matter, sheep faeces was sandwiched between two halves of intact soil cores and incubated at 20°C. The soils contained 10.8 (L1), 22.4 (L3) and 33.7% (L5) clay, respectively, and were drained to seven different matric potentials in the range –15 to –1500 hPa. Evolution of CO2-C was determined during four weeks of incubation. Contents of NO3-N, 15N and microbial biomass N were determine...

  16. Renal ischemia and reperfusion assessment with three-dimensional hyperpolarized (13) C,(15) N2-urea

    Nielsen, Per Mose; Szocska Hansen, Esben Søvsø; Nørlinger, Thomas Stokholm;

    2016-01-01

    . METHODS: Hyperpolarized three-dimensional balanced steady-state (13) C magnetic resonance imaging (MRI) experiments alongside kidney function parameters and quantitative polymerase chain reaction measurements were performed in rats subjected to unilateral renal ischemia for 60-minute and 24-hour......,(15) N2 urea MRI can be used to successfully detect changes in the intrarenal urea gradient post-IRI, thereby enabling in vivo monitoring of the intrarenal functional status in the rat kidney. Magn Reson Med, 2016. © 2016 International Society for Magnetic Resonance in Medicine....

  17. Binary reaction channels in the 12C+19F and 16O+15N nuclear collisions

    The 19F on 12C and 15N on 16O reactions are studied not only in order to search for resonances but furthermore to perform a comparative study of binary reaction channels in two collisions leading to the same excitation energies of the composite system. The main feature of the experimental procedure is an exclusive detection of the two fragments in the exit channel using the kinematical coincidence method. Angular distributions and excitation functions of the main binary channels are presented and discussed

  18. Uptake of stormwater nitrogen in bioretention systems demonstrated from 15N tracer techniques

    Houdeshel, D.; Hultine, K. R.; Pomeroy, C. A.

    2012-12-01

    Bioretention stormwater management systems are engineered ecosystems that capture urban stormwater in order to reduce the harmful effects of stormwater pollution on receiving waters. Bioretention systems have been shown to be effective at reducing the volume of runoff, and thereby reduce the nutrient loading to receiving waters from urban areas. However, little work has been done to evaluate the treatment processes that are responsible for reductions in effluent nitrogen (N). We hypothesize that the pulses of inorganic nitrogen associated with urban runoff events are captured in the plat tissues within these systems and not adsorbed to the soil media, thus creating a long-term, sustainable treatment approach to reducing the total nutrient loading to receiving waters. Nitrogen treatment performance was tested on two bioretention systems in Salt Lake City, UT: 1) an upland native community that does not require irrigation in semi-arid climates, and 2) a wetland community that requires 250 l of daily irrigation to offset the relatively high evaporative demand in the region. Each cell is sized to treat a 2.5 cm storm from a 140 m2 impervious surface: the area of the bioretention system is 10 m2. To test the N removal performance of each system, runoff events were simulated to represent an average precipitation regime using a synthetic stormwater blend starting in January, 2012. Effluent was collected from an underdrain and analyzed for total nitrogen (TN); mass removal was calculated for each month by subtracting the TN mass added to the garden minus the TN mass that flowed out of the garden. To test the hypothesis that plants assimilate stormwater N, 4 g of 100 atom% 15N NH4NO3 tracer was used as the N source in the synthetic stormwater during the first 2,000 l synthetic storm event in May. This isotopic label was calculated to enrich the total N pool of each garden to 100‰ 15N/14Nair. New growth was harvested from each plant in both cells and analyzed for 15N

  19. Optical Microscopy Characterization for Borehole U-15n#12 in Support of NCNS Source Physics Experiment

    Wilson, Jennifer E. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Sussman, Aviva Joy [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-05-22

    Optical microscopy characterization of thin sections from corehole U-15n#12 is part of a larger material characterization effort for the Source Physics Experiment (SPE). The SPE program was conducted in Nevada with a series of explosive tests designed to study the generation and propagation of seismic waves inside Stock quartz monzonite. Optical microscopy analysis includes the following: 1) imaging of full thin sections (scans and mosaic maps); 2) high magnification imaging of petrographic texture (grain size, foliations, fractures, etc.); and 3) measurement of microfracture density.

  20. The $^{15}$N($\\bm\\alpha$,$\\bm\\gamma$)$^{19}$F reaction and nucleosynthesis of $^{19}$F

    Wilmes, S.; Wilmes, V.; Staudt, G.; Mohr, P; Hammer, J. W.

    2002-01-01

    Several resonances in the $^{15}$N($\\alpha$,$\\gamma$)$^{19}$F reaction have been investigated in the energy range between 0.6 MeV and 2.7 MeV. Resonance strengths and branching ratios have been determined. High sensitivity could be obtained by the combination of the {\\sc{dynamitron}} high current accelerator, the windowless gas target system {\\sc{rhinoceros}}, and actively shielded germanium detectors. Two levels of $^{19}$F could be observed for the first time in the ($\\alpha$,$\\gamma$) chan...

  1. Determination of the δ15N of nitrate in solids; RSIL lab code 2894

    Coplen, Tyler B.; Qi, Haiping; Revesz, Kinga; Casciotti, Karen; Hannon, Janet E.

    2007-01-01

    The purpose of the Reston Stable Isotope Laboratory (RSIL) lab code 2894 is to determine the δ15N of nitrate (NO3-) in solids. The nitrate fraction of the nitrogen species is dissolved by water (called leaching) and can be analyzed by the bacterial method covered in RSIL lab code 2899. After leaching, the δ15N of the dissolved NO3- is analyzed by conversion of the NO3- to nitrous oxide (N2O), which serves as the analyte for mass spectrometry. A culture of denitrifying bacteria is used in the enzymatic conversion of NO3- to N2O, which follows the pathway shown in equation 1: NO3- → NO2- → NO → 1/2 N2O (1) Because the bacteria Pseudomonas aureofaciens lack N2O reductive activity, the reaction stops at N2O, unlike the typical denitrification reaction that goes to N2. After several hours, the conversion is complete, and the N2O is extracted from the vial, separated from volatile organic vapor and water vapor by an automated -65 °C isopropanol-slush trap, a Nafion drier, a CO2 and water removal unit (Costech #021020 carbon dioxide absorbent with Mg(ClO4)2), and trapped in a small-volume trap immersed in liquid nitrogen with a modified Finnigan MAT (now Thermo Scientific) GasBench 2 introduction system. After the N2O is released, it is further purified by gas chromatography before introduction to the isotope-ratio mass spectrometer (IRMS). The IRMS is a Thermo Scientific Delta V Plus continuous flow IRMS (CF-IRMS). It has a universal triple collector, consisting of two wide cups with a narrow cup in the middle; it is capable of simultaneously measuring mass/charge (m/z) of the N2O molecule 44, 45, and 46. The ion beams from these m/z values are as follows: m/z = 44 = N2O = 14N14N16O; m/z = 45 = N2O = 14N15N16O or 14N14N17O; m/z = 46 = N2O = 14N14N18O. The 17O contributions to the m/z 44 and m/z 45 ion beams are accounted for before δ15N values are reported.

  2. Determination of the δ15N of nitrate in water; RSIL lab code 2899

    Coplen, Tyler B.; Qi, Haiping; Revesz, Kinga; Casciotti, Karen; Hannon, Janet E.

    2007-01-01

    The purpose of the Reston Stable Isotope Laboratory (RSIL) lab code 2899 is to determine the δ15N of nitrate (NO3-) in water. The δ15N of the dissolved NO3- is analyzed by conversion of the NO3- to nitrous oxide (N2O), which serves as the analyte for mass spectrometry. A culture of denitrifying bacteria is used in the enzymatic conversion of the NO3- to N2O, which follows the pathway shown in equation 1: NO3- → NO2- → NO → 1/2 N2O (1) Because the bacteria Pseudomonas aureofaciens lack N2O reductive activity, the reaction stops at N2O, unlike the typical denitrification reaction that goes to N2. After several hours, the conversion is complete, and the N2O is extracted from the vial, separated from volatile organic vapor and water vapor by an automated -65 °C isopropanol-slush trap, a Nafion drier, a CO2 and water removal unit (Costech #021020 carbon dioxide absorbent with Mg(ClO4)2), and trapped in a small-volume trap immersed in liquid nitrogen with a modified Finnigan MAT (now Thermo Scientific) GasBench 2 introduction system. After the N2O is released, it is further purified by gas chromatography before introduction to the isotope-ratio mass spectrometer (IRMS). The IRMS is a Thermo Scientific Delta V Plus continuous flow IRMS (CF-IRMS). It has a universal triple collector, consisting of two wide cups with a narrow cup in the middle; it is capable of simultaneously measuring mass/charge (m/z) of the N2O molecule 44, 45, and 46. The ion beams from these m/z values are as follows: m/z = 44 = N2O = 14N14N16O; m/z = 45 = N2O = 14N15N16O or 14N14N17O; m/z = 46 = N2O = 14N14N18O. The 17O contributions to the m/z 44 and m/z 45 ion beams are accounted for before δ15N values are reported.

  3. Feasibility analysis of organic Tea authentication using 15N natural abundance method

    Organic agricultural products were always adulterated by pollutant-free agricultural products in market because of lacking of available authentication technique. Organic tea was one of the largest organic agricultural products in China which are facing the same problem and can not be accepted by consumers. In this paper, based on the newest information of δ 15N from soil-plant-fertilizer system, a new method was suggested to identify whether N fertilizer was applied to organic tea in producing processing. Meanwhile, the principle of this new method and its feasibility were discussed. (authors)

  4. Effect of estrogens on urinary /sup 15/N balance in girls

    Zachmann, M.; Kempken, B.; Prader, A. (Zurich Univ. (Switzerland))

    1984-08-01

    While the anabolic and growth-promoting effects of testosterone are known to be important for pubertal growth in boys, the role of estrogens (E) in the female spurt is less certain. Adrenal androgens have been considered to be more important than ovarian E. To study the anabolic effects of E, there has been carried out a pilot study in 9 girls aged 11 to 15 years. Before and 6 days after the start of E treatment, urinary /sup 15/N balance studies were performed, using /sup 15/NH/sub 4/Cl.

  5. Constructing Battery-Aware Virtual Backbones in Wireless Sensor Networks

    Chi Ma

    2007-05-01

    Full Text Available A critical issue in battery-powered sensor networks is to construct energy efficient virtual backbones for network routing. Recent study in battery technology reveals that batteries tend to discharge more power than needed and reimburse the over-discharged power if they are recovered. In this paper we first provide a mathematical battery model suitable for implementation in sensor networks. We then introduce the concept of battery-aware connected dominating set (BACDS and show that in general the minimum BACDS (MBACDS can achieve longer lifetime than the previous backbone structures. Then we show that finding a MBACDS is NP-hard and give a distributed approximation algorithm to construct the BACDS. The resulting BACDS constructed by our algorithm is at most (8+Δopt size, where Δ is the maximum node degree and opt is the size of an optimal BACDS. Simulation results show that the BACDS can save a significant amount of energy and achieve up to 30% longer network lifetime than previous schemes.

  6. Long-term forecasting of internet backbone traffic.

    Papagiannaki, Konstantina; Taft, Nina; Zhang, Zhi-Li; Diot, Christophe

    2005-09-01

    We introduce a methodology to predict when and where link additions/upgrades have to take place in an Internet protocol (IP) backbone network. Using simple network management protocol (SNMP) statistics, collected continuously since 1999, we compute aggregate demand between any two adjacent points of presence (PoPs) and look at its evolution at time scales larger than 1 h. We show that IP backbone traffic exhibits visible long term trends, strong periodicities, and variability at multiple time scales. Our methodology relies on the wavelet multiresolution analysis (MRA) and linear time series models. Using wavelet MRA, we smooth the collected measurements until we identify the overall long-term trend. The fluctuations around the obtained trend are further analyzed at multiple time scales. We show that the largest amount of variability in the original signal is due to its fluctuations at the 12-h time scale. We model inter-PoP aggregate demand as a multiple linear regression model, consisting of the two identified components. We show that this model accounts for 98% of the total energy in the original signal, while explaining 90% of its variance. Weekly approximations of those components can be accurately modeled with low-order autoregressive integrated moving average (ARIMA) models. We show that forecasting the long term trend and the fluctuations of the traffic at the 12-h time scale yields accurate estimates for at least 6 months in the future. PMID:16252820

  7. Controlled Conjugated Backbone Twisting for an Increased Open-Circuit Voltage while Having a High Short-Circuit Current in Poly(hexylthiophene) Derivatives

    Ko, Sangwon

    2012-03-21

    Conjugated polymers with nearly planar backbones have been the most commonly investigated materials for organic-based electronic devices. More twisted polymer backbones have been shown to achieve larger open-circuit voltages in solar cells, though with decreased short-circuit current densities. We systematically impose twists within a family of poly(hexylthiophene)s and examine their influence on the performance of polymer:fullerene bulk heterojunction (BHJ) solar cells. A simple chemical modification concerning the number and placement of alkyl side chains along the conjugated backbone is used to control the degree of backbone twisting. Density functional theory calculations were carried out on a series of oligothiophene structures to provide insights on how the sterically induced twisting influences the geometric, electronic, and optical properties. Grazing incidence X-ray scattering measurements were performed to investigate how the thin-film packing structure was affected. The open-circuit voltage and charge-transfer state energy of the polymer:fullerene BHJ solar cells increased substantially with the degree of twist induced within the conjugated backbone-due to an increase in the polymer ionization potential-while the short-circuit current decreased as a result of a larger optical gap and lower hole mobility. A controlled, moderate degree of twist along the poly(3,4-dihexyl-2,2′:5′,2′′- terthiophene) (PDHTT) conjugated backbone led to a 19% enhancement in the open-circuit voltage (0.735 V) vs poly(3-hexylthiophene)-based devices, while similar short-circuit current densities, fill factors, and hole-carrier mobilities were maintained. These factors resulted in a power conversion efficiency of 4.2% for a PDHTT:[6,6]-phenyl-C 71-butyric acid methyl ester (PC 71BM) blend solar cell without thermal annealing. This simple approach reveals a molecular design avenue to increase open-circuit voltage while retaining the short-circuit current. © 2012 American

  8. General order parameter based correlation analysis of protein backbone motions between experimental NMR relaxation measurements and molecular dynamics simulations

    Internal backbone dynamic motions are essential for different protein functions and occur on a wide range of time scales, from femtoseconds to seconds. Molecular dynamic (MD) simulations and nuclear magnetic resonance (NMR) spin relaxation measurements are valuable tools to gain access to fast (nanosecond) internal motions. However, there exist few reports on correlation analysis between MD and NMR relaxation data. Here, backbone relaxation measurements of 15N-labeled SH3 (Src homology 3) domain proteins in aqueous buffer were used to generate general order parameters (S2) using a model-free approach. Simultaneously, 80 ns MD simulations of SH3 domain proteins in a defined hydrated box at neutral pH were conducted and the general order parameters (S2) were derived from the MD trajectory. Correlation analysis using the Gromos force field indicated that S2 values from NMR relaxation measurements and MD simulations were significantly different. MD simulations were performed on models with different charge states for three histidine residues, and with different water models, which were SPC (simple point charge) water model and SPC/E (extended simple point charge) water model. S2 parameters from MD simulations with charges for all three histidines and with the SPC/E water model correlated well with S2 calculated from the experimental NMR relaxation measurements, in a site-specific manner. - Highlights: • Correlation analysis between NMR relaxation measurements and MD simulations. • General order parameter (S2) as common reference between the two methods. • Different protein dynamics with different Histidine charge states in neutral pH. • Different protein dynamics with different water models

  9. General order parameter based correlation analysis of protein backbone motions between experimental NMR relaxation measurements and molecular dynamics simulations

    Liu, Qing; Shi, Chaowei [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); Yu, Lu [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); High Magnetic Field Laboratory, Chinese Academy of Science, Hefei, Anhui, 230031 (China); Zhang, Longhua [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); Xiong, Ying, E-mail: yxiong73@ustc.edu.cn [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); Tian, Changlin, E-mail: cltian@ustc.edu.cn [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); High Magnetic Field Laboratory, Chinese Academy of Science, Hefei, Anhui, 230031 (China)

    2015-02-13

    Internal backbone dynamic motions are essential for different protein functions and occur on a wide range of time scales, from femtoseconds to seconds. Molecular dynamic (MD) simulations and nuclear magnetic resonance (NMR) spin relaxation measurements are valuable tools to gain access to fast (nanosecond) internal motions. However, there exist few reports on correlation analysis between MD and NMR relaxation data. Here, backbone relaxation measurements of {sup 15}N-labeled SH3 (Src homology 3) domain proteins in aqueous buffer were used to generate general order parameters (S{sup 2}) using a model-free approach. Simultaneously, 80 ns MD simulations of SH3 domain proteins in a defined hydrated box at neutral pH were conducted and the general order parameters (S{sup 2}) were derived from the MD trajectory. Correlation analysis using the Gromos force field indicated that S{sup 2} values from NMR relaxation measurements and MD simulations were significantly different. MD simulations were performed on models with different charge states for three histidine residues, and with different water models, which were SPC (simple point charge) water model and SPC/E (extended simple point charge) water model. S{sup 2} parameters from MD simulations with charges for all three histidines and with the SPC/E water model correlated well with S{sup 2} calculated from the experimental NMR relaxation measurements, in a site-specific manner. - Highlights: • Correlation analysis between NMR relaxation measurements and MD simulations. • General order parameter (S{sup 2}) as common reference between the two methods. • Different protein dynamics with different Histidine charge states in neutral pH. • Different protein dynamics with different water models.

  10. Homogeneity of δ15N in needles of Masson pine (Pinus massoniana L.) was altered by air pollution

    The present study investigated the changes of δ15N values in the tip, middle and base section (divided by the proportion to needle length) of current- and previous-year needles of Masson pine (Pinus massoniana L.) from two declining forest stands suffering from air pollution, in comparison with one healthy stand. At the healthy stand, δ15N in the three sections of both current- and previous-year needles were found evenly distributed, while at the polluted stands, δ15N values in the needles were revealed significantly different from the tip to the base sections. The results implied that the distribution of δ15N among different parts or sections in foliages was not always homogeneous and could be affected by air pollution. We suggested that the difference of δ15N values among pine needle sections should be reconsidered and should not be primarily ignored when the needle δ15N values were used to assess plant responses to air pollution. - Values of δ15N in needles of Masson pine (Pinus massoniana L.) were uneven and affected by air pollution.

  11. Effect of four plant species on soil 15N-access and herbage yield in temporary agricultural grasslands

    Pirhofter-Walzl, Karin; Eriksen, Jørgen; Rasmussen, Jim;

    2013-01-01

    . This positive plant diversity effect could not be explained by complementary soil 15N-access of the different plant species from 0.4, 0.8 and 1.2 m soil depths, even though deep-rooting chicory acquired relatively large amounts of deep soil 15N and shallow-rooting perennial ryegrass when grown in a...... access to greater amounts of soil 15N compared with a shallow-rooting binary mixture, and if leguminous plants affect herbage yield and soil 15N-access. Methods 15N-enriched ammonium-sulphate was placed at three different soil depths (0.4, 0.8 and 1.2 m) to determine the depth dependent soil 15N......-access of pure stands, two-species and four-species grassland communities. Results Herbage yield and soil 15N-access of the mixture including deep- and shallow-rooting grassland species were generally greater than the pure stands and the two-species mixture, except for herbage yield in pure stand lucerne...

  12. {sup 15}N-labeled nitrogen from green manure and ammonium sulfate utilization by the sugarcane ratoon

    Ambrosano, Edmilson Jose; Rossi, Fabricio, E-mail: ambrosano@apta.sp.gov.b [Agencia Paulista de Tecnologia dos Agronegocios (APTA), Piracicapa, SP (Brazil). Polo Rigional Centro Sul; Trivelin, Paulo Cesar Ocheuze [Centro de Energia Nuclear na Agricultura (CENA/USP), Piracicaba, SP (Brazil). Lab. de Isotopos Estaveis; Cantarella, Heitor [Agencia Paulista de Tecnologia dos Agronegocios (APTA/IAC), Campinas, SP (Brazil). Instituto Agronomico de Campinas. Centro de Solos e Recursos Agroambientais; Ambrosano, Glaucia Maria Bovi [Universidade de Campinas (UNICAMP/FOP), Piracicaba, SP (Brazil). Fac. de Odontologia de Piracicaba. Dept. de Odontologia Social, Bioestatistica; Schammass, Eliana Aparecida [Agencia Paulista de Tecnologia dos Agronegocios (APTA/IZ), Nova Odessa, SP (Brazil). Instituto de Zootecnia; Muraoka, Takashi [Centro de Energia Nuclear na Agricultura (CENA/USP), Piracicaba, SP (Brazil). Lab. de Fertilidade do solo

    2011-05-15

    Legumes as green manure are alternative sources of nitrogen (N) for crops and can supplement or even replace mineral nitrogen fertilization due to their potential for biological nitrogen fixation (BNF). The utilization of nitrogen by sugarcane (Saccharum spp.) fertilized with sunn hemp (Crotalaria juncea L.) and ammonium sulfate (AS) was evaluated using the {sup 15}N tracer technique. N was added at the rate of 196 and 70 kg ha{sup -1} as {sup 15}N-labeled sunn hemp green manure (SH) and as ammonium sulfate (AS), respectively. Treatments were: (I) Control; (II) AS{sup 15}N; (III) SH{sup 15}N + AS; (IV) SH{sup 15}N; and (V) AS{sup 15}N + SH. Sugarcane was cultivated for five years and was harvested three times. {sup 15}N recovery was evaluated in the two first harvests. In the sum of the three harvests, the highest stalk yields were obtained with a combination of green manure and inorganic N fertilizer; however, in the second cutting the yields were higher where SH was used than in plots with AS. The recovery of N by the first two consecutive harvests accounted for 19 to 21% of the N applied as leguminous green manure and 46 to 49% of the N applied as AS. The amounts of inorganic N, derived from both N sources, present in the 0-0.4 m layer of soil in the first season after N application and were below 1 kg ha{sup -1}. (author)

  13. {delta}{sup 15}N of seagrass leaves for monitoring anthropogenic nutrient increases in coral reef ecosystems

    Yamamuro, M.; Kayanne, H.; Yamano, H

    2003-04-01

    In a coral reef environment, a slight increase in dissolved inorganic nitrogen (DIN;{>=}1.0 {mu}M) can alter the ecosystem via macroalgal blooms. We collected seagrass leaves from the tropical and subtropical Pacific Ocean in five countries and examined the interactions between nutrient concentrations (C, N, P), molar ratios of nutrients, and {delta}{sup 15}N to find a possible indicator of the DIN conditions. Within most sites, the concentrations of nutrients and their molar ratios showed large variations owing to species-specific values. On the other hand, almost identical {delta}{sup 15}N values were found in seagrass leaves of several species at each site. The correlations between {delta}{sup 15}N and nutrient concentrations and between {delta}{sup 15}N and molar ratios of nutrients suggested that nutrient availability did not affect the {delta}{sup 15}N value of seagrass leaves by altering the physiological condition of the plants. Increases in {delta}{sup 15}N of seagrass leaves mostly matched increases in DIN concentrations in the bottom water. We suggest that {delta}{sup 15}N in seagrass leaves can be a good tool to monitor time-integrated decrease/increase of DIN concentrations at a site, both in the water column and the interstitial water.

  14. Estimation of symbiotic dinitrogen fixation in alder forest by the method based on natural 15N abundance

    Annual N2-fixation in virgin forest ecosystems has been measured using a 15N natural abundance (δ15N)procedure. This method was compared to a 15N labelled fertilizer isotopic dilution method. For young alders (5-6 years old), δ15N of leaves gave results in good agreement with the isotopic dilution of fertilizer method. Since δ15N variability was expected according to plant physiology, for alder trees, leaves were collected at various heights after the end of the growing season, and, to take account of isotopic variations coming from derived inputs, δ15N of leaves of a large number of other plants in the same area were measured to give control values. Following this procedure, the δ15N method gave reliable evaluation of the nitrogen supply, by through N2-fixation, to alders, which were found to maintain high nitrogen fixing capacity in a sequence ranging from first stage of establishment of climactic formation. Moreover, the same method is reported to discriminate various origins of Alnus glutinosa grown in natural conditions, possibly in relation to the genetic diversity of this species. (author). 22 refs., 3 figs., 2 tabs

  15. Oligomeric complexes of some heteroaromatic ligands and aromatic diamines with rhodium and molybdenum tetracarboxylates: 13C and 15N CPMAS NMR and density functional theory studies.

    Leniak, Arkadiusz; Kamieński, Bohdan; Jaźwiński, Jarosław

    2015-05-01

    Seven new oligomeric complexes of 4,4'-bipyridine; 3,3'-bipyridine; benzene-1,4-diamine; benzene-1,3-diamine; benzene-1,2-diamine; and benzidine with rhodium tetraacetate, as well as 4,4'-bipyridine with molybdenum tetraacetate, have been obtained and investigated by elemental analysis and solid-state nuclear magnetic resonance spectroscopy, (13)C and (15)N CPMAS NMR. The known complexes of pyrazine with rhodium tetrabenzoate, benzoquinone with rhodium tetrapivalate, 4,4'-bipyridine with molybdenum tetrakistrifluoroacetate and the 1 : 1 complex of 2,2'-bipyridine with rhodium tetraacetate exhibiting axial-equatorial ligation mode have been obtained as well for comparison purposes. Elemental analysis revealed 1 : 1 complex stoichiometry of all complexes. The (15)N CPMAS NMR spectra of all new complexes consist of one narrow signal, indicating regular uniform structures. Benzidine forms a heterogeneous material, probably containing linear oligomers and products of further reactions. The complexes were characterized by the parameter complexation shift Δδ (Δδ = δcomplex  - δligand). This parameter ranged from around -40 to -90 ppm in the case of heteroaromatic ligands, from around -12 to -22 ppm for diamines and from -16 to -31 ppm for the complexes of molybdenum tetracarboxylates with 4,4'-bipyridine. The experimental results have been supported by a density functional theory computation of (15)N NMR chemical shifts and complexation shifts at the non-relativistic Becke, three-parameter, Perdew-Wang 91/[6-311++G(2d,p), Stuttgart] and GGA-PBE/QZ4P levels of theory and at the relativistic scalar and spin-orbit zeroth order regular approximation/GGA-PBE/QZ4P level of theory. Nucleus-independent chemical shifts have been calculated for the selected compounds. PMID:25614975

  16. Studies on nitrogen use efficiency in turmeric using 15N tagged urea

    A greenhouse experiment was conducted with turmeric in order to understand the partitioning of N between shoot and rhizome and to study the N use efficiency using 15N tagged urea. The experiment was conducted in a completely randomized block design with seven treatments consisting of whole N application as basal and split applications ranging from two to six, besides a control. The result indicated that N derived from 15N urea (Ndff) increased with number of split application of N up to four splits in turmeric shoot and up to three splits in turmeric rhizome, both at 180 days as well as at harvest stage. Increasing the splits beyond this declined Ndff, which indicated that five and more number of splits of N would not help to increase the uptake of applied N. Thus, the present study clearly revealed that in turmeric, application of N in three splits would be optimal in increasing the Ndff in rhizome. Fertilizer N balance calculations clearly indicated that the recovery of N in turmeric was high in favour of four splits at 180 days growth stage (19.46 per cent) as well as at harvest (30.76 per cent). (author)

  17. 15N isotopic techniques to study nitrogen cycle in soil-plant-atmosphere system

    Intensification of agriculture to meet the increasing food demand has caused severe disruption in natural balance of global as well as regional nitrogen cycle, potentially threatening the future sustainability of agriculture and environment of the total fertilizer nitrogen used in agriculture globally, only less than half is recovered by crop plants, rest is lost to the environment, resulting in several environmental problems such as ground water pollution and global warming, besides huge economic loss of this costly input in agriculture. Improving fertilizer nitrogen use efficiency and minimising N loss to the environment is the key to regain the lost control of nitrogen cycle in agriculture. Fertilizer nitrogen use efficiency depends largely on N requirement of crops, N supply from soil and fertilizer through N transformations in soil, and N losses from the soil-water-plant system. 15N isotopic techniques have the potential to provide accurate measurement quantification of different processes involved in N cycle such as fixation of atmospheric N2, transformations- mineralization and immobilization- of soil and fertilizer N which governs N supply to plants, and N losses to the environment through ammonia volatilization, denitrification and nitrate leaching. 15N tracers can also give precise identification of ways and sources of N loss from agriculture. These information can be used to develop strategies for increasing fertilizer N use efficiency and minimizing the loss of this costly input from agriculture to environment, which in turn will help to achieve the tripartite goal of food security, agricultural profitability and environmental quality. (author)

  18. Growth, development, and fertilizer-15N recovery by the coffee plant

    The relationship between growth and fertilizer nitrogen recovery by perennial crops such as coffee is poorly understood and improved understanding of such relations is important for the establishment of rational crop management practices. In order to characterize the growth of a typical coffee crop in Brazil and quantify the recovery of 15N labeled ammonium sulfate, and improve information for fertilizer management practices this study presents results for two consecutive cropping years, fertilized with 280 and 350 kg ha-1 of N, respectively, applied in four splittings, using five replicates. Shoot dry matter accumulation was evaluated every 60 days, separating plants into branches, leaves and fruits. Labeled sub-plots were used to evaluate N-total and 15N abundance by mass spectrometry. During the first year the aerial part reached a recovery of 71% of the fertilizer N applied up to February, but this value was reduced to 34% at harvest and 19% at the beginning of the next flowering period due to leaf fall and fruit export. For the second year the aerial part absorbed 36% of the fertilizer N up to March, 47% up to harvest and 19% up to the beginning of the next flowering period. The splitting into four applications of the used fertilizer rates was adequate for the requirements of the crop at these growth stages of the coffee crop. (author)

  19. Effects of [15N]leucine infused at low rates on leucine metabolism in humans

    The present studies were carried out to determine whether infusions of [15N]leucine at low rates affect estimates of leucine oxidation and of proteolysis and protein synthesis in humans. Three groups of normal subjects were infused for 3 h with either [15N]leucine at a rate of 0.16 or 0.26 mumol X kg-1 X min-1 or saline using [3H]leucine and alpha-[14C]ketoisocaproate as isotopic tracers of leucine metabolism. Data were analyzed at steady state using both single- and dual-isotope models. Preliminary studies were carried out to characterize the dual-isotope model in humans using infusions of [3H]leucine and alpha-[14C]ketoisocaproate. In the postabsorptive state estimates of leucine appearance, disappearance, and oxidation derived from the two isotope models were in good agreement. Infusion of stable isotope up to approximately 10% of the leucine carbon flux do not have a significant effect on leucine metabolism, but the data derived from such studies must be properly controlled and interpreted with care because these tracers are not massless

  20. Distribution of spin dipole transition strength in the 15N(n,p)15C reaction

    The reaction 15N(n,p)15C was studied at a neutron energy of 288 MeV using the TRIUMF (n,p) charge exchange facility and a high pressure gas target. The angular distributions for spin dipole (ΔL=1) transitions to the states in 15C at energies 0 MeV and 0.740 MeV, as well as for higher excitation energies, were measured and the results were compared with DWIA calculations. The measured distribution of the spin dipole strength agrees well with shell model predictions, indicating that a rather simple model provides a satisfactory description of the 15N ground state, and of positive parity states in 15C up to about 18 MeV excitation. The magnitude of the peak cross sections (at ≅ 7 degrees) is described well by the calculations when the theoretical cross section is renormalized by a factor 0.7. The calculated cross sections near zero degrees are generally smaller than experimental data. It this is a general feature of ΔL=1 transitions, it suggests that estimates of GT strength based on a multipole decomposition of measured cross sections may be too high. (Author) (41 refs., 3 tabs., 14 figs.)

  1. Oxygen determination in materials by 18O(p,αγ)15N nuclear reaction

    Kumar, Sanjiv; Sunitha, Y.; Reddy, G. L. N.; Sukumar, A. A.; Ramana, J. V.; Sarkar, A.; Verma, Rakesh

    2016-07-01

    The paper presents a proton induced γ-ray emission method based on 18O(p,αγ)15N nuclear reaction to determine bulk oxygen in materials. The determination involves the measurement of 5.27 MeV γ-rays emitted following the de-excitation of 15N nuclei. A description of the energetics of the reaction is given to provide an insight into the origin of 5.27 MeV γ-rays. In addition, thick target γ-ray yields and the limits of detection are measured to ascertain the analytical potential of the reaction. The thick-target γ-ray yields are measured with a high purity germanium detector and a bismuth germanate detector at 0° as well as 90° angles in 3.0-4.2 MeV proton energy region. The best limit of detection of about 1.3 at.% is achieved at 4.2 MeV proton energy for measurements at 0° as well 90° angles with the bismuth germanate detector while the uncertainty in quantitative analysis is oxygen in several oxide as well as non-oxide materials.

  2. Growth, development, and fertilizer-{sup 15}N recovery by the coffee plant

    Fenilli, Tatiele Anete Bergamo [Fundacao Universidade Regional de Blumenau (FURB), Blumenau, SC (Brazil). Dept. de Engenharia Florestal; Reichardt, Klaus; Bacchi, Osny Oliveira Santos [Centro de Energia Nuclear na Agricultura (CENA), Piracicaba, SP (Brazil). Lab. de Fisica do Solo]. E-mail: klaus@cena.usp.br; Dourado-Neto, Durval; Favarin, Jose Laercio [Escola Superior de Agricultura Luiz de Queiroz (ESALQ/USP), Piracicaba, SP (Brazil). Dept. de Producao Vegetal; Trivelim, Paulo Cesar Ocheuze [Centro de Energia Nuclear na Agricultura (CENA), Piracicaba, SP (Brazil). Lab. de Isotopos Estaveis; Costa, Flavio Murilo Pereira da [Ministerio do Desenvolvimento Agrario, Brasilia, DF (Brazil). Secretaria de Assuntos Fundiarios - SEAF

    2007-09-15

    The relationship between growth and fertilizer nitrogen recovery by perennial crops such as coffee is poorly understood and improved understanding of such relations is important for the establishment of rational crop management practices. In order to characterize the growth of a typical coffee crop in Brazil and quantify the recovery of {sup 15}N labeled ammonium sulfate, and improve information for fertilizer management practices this study presents results for two consecutive cropping years, fertilized with 280 and 350 kg ha{sup -1} of N, respectively, applied in four splittings, using five replicates. Shoot dry matter accumulation was evaluated every 60 days, separating plants into branches, leaves and fruits. Labeled sub-plots were used to evaluate N-total and {sup 15}N abundance by mass spectrometry. During the first year the aerial part reached a recovery of 71% of the fertilizer N applied up to February, but this value was reduced to 34% at harvest and 19% at the beginning of the next flowering period due to leaf fall and fruit export. For the second year the aerial part absorbed 36% of the fertilizer N up to March, 47% up to harvest and 19% up to the beginning of the next flowering period. The splitting into four applications of the used fertilizer rates was adequate for the requirements of the crop at these growth stages of the coffee crop. (author)

  3. MUSIC in triple-resonance experiments: amino acid type-selective (1)H-(15)N correlations

    Schubert; Smalla; Schmieder; Oschkinat

    1999-11-01

    Amino acid type-selective triple-resonance experiments can be of great help for the assignment of protein spectra, since they help to remove ambiguities in either manual or automated assignment procedures. Here, modified triple-resonance experiments that yield amino acid type-selective (1)H-(15)N correlations are presented. They are based on novel coherence transfer schemes, the MUSIC pulse sequence elements, that replace the initial INEPT transfer and are selective for XH(2) or XH(3) (X can be (15)N or (13)C). The desired amino acid type is thereby selected based on the topology of the side chain. Experiments for Gly (G-HSQC); Ala (A-HSQC); Thr, Val, Ile, and Ala (TAVI-HSQC); Thr and Ala (TA-HSQC), as well as Asn and Gln (N-HSQC and QN-HSQC), are described. The new experiments are recorded as two-dimensional experiments and therefore need only small amounts of spectrometer time. The performance of the experiments is demonstrated with the application to two protein domains. Copyright 1999 Academic Press. PMID:10527741

  4. Constraining the S factor of 15N(p,g)16O at Astrophysical Energies

    LeBlanc, P J; Goerres, J; Junker, M; Azuma, R; Beard, M; Bemmerer, D; Best, A; Broggini, C; Caciolli, A; Corvisiero, P; Costantini, H; Couder, M; deBoer, R; Elekes, Z; Falahat, S; Formicola, A; Fulop, Zs; Gervino, G; Guglielmetti, A; Gustavino, C; Gyurky, Gy; Kaeppeler, F; Kontos, A; Kuntz, R; Leiste, H; Lemut, A; Li, Q; Limata, B; Marta, M; Mazzocchi, C; Menegazzo, R; O'Brien, S; Palumbo, A; Prati, P; Roca, V; Rolfs, C; Alvarez, C Rossi; Somorjai, E; Stech, E; Straniero, O; Strieder, F; Tan, W; Terrasi, F; Trautvetter, H P; Uberseder, E; Wiescher, M

    2010-01-01

    The 15N(p,g)16O reaction represents a break out reaction linking the first and second cycle of the CNO cycles redistributing the carbon and nitrogen abundances into the oxygen range. The reaction is dominated by two broad resonances at Ep = 338 keV and 1028 keV and a Direct Capture contribution to the ground state of 16O. Interference effects between these contributions in both the low energy region (Ep < 338 keV) and in between the two resonances (338 15N(p,g)16O reaction has been remeasured covering the energy range from Ep=1800 keV down to 130 keV. The results have been analyzed in the framework of a multi-level R-matrix theory and a S(0) value of 39.6 keV b has been found.

  5. Nutritional status of sugar cane (planted cane) in 15N experiments

    Studies with stable isotopes are becoming more common due to the increased safety of operation and quality and reliability of results. However, the use of microplots is required to decrease the costs of such studies. Since microplots are small compared to regular plot areas, the purpose of this study was to investigate whether nutritional data based on microplot samples can adequately represent the whole area, in a comparison of the nutritional status of microplot sugar cane plants at their maximum development stage with those of the regular plots in experiments with N rates. Three experiments were set up, with three N rates (40, 80, and 120 kg ha-1 N) and a control, with four repetitions, in a randomized complete block design, in the state of Sao Paulo. Microplots of 3 m2 containing 15N-fertilizer (5.04% atom 15N) were included in the main plots formed by 48 lines of sugar cane spaced 1.5 m apart. At the time of maximum development stage, diagnostic leaves were collected in the main and microplots to evaluate the nutritional status of plants by analyzing the total concentration of macro nutrients. There were no differences in N, P, Ca, Mg, and S concentrations in the diagnostic leaves from the main and microplots, so that the latter can be considered representative of the experimental area. Higher nitrogen fertilizer rates induced increased concentrations of not only N, but also of P, Ca, Mg, and S in the diagnostic leaves. (author)

  6. MUSIC in Triple-Resonance Experiments: Amino Acid Type-Selective 1H- 15N Correlations

    Schubert, Mario; Smalla, Maika; Schmieder, Peter; Oschkinat, Hartmut

    1999-11-01

    Amino acid type-selective triple-resonance experiments can be of great help for the assignment of protein spectra, since they help to remove ambiguities in either manual or automated assignment procedures. Here, modified triple-resonance experiments that yield amino acid type-selective 1H-15N correlations are presented. They are based on novel coherence transfer schemes, the MUSIC pulse sequence elements, that replace the initial INEPT transfer and are selective for XH2 or XH3 (X can be 15N or 13C). The desired amino acid type is thereby selected based on the topology of the side chain. Experiments for Gly (G-HSQC); Ala (A-HSQC); Thr, Val, Ile, and Ala (TAVI-HSQC); Thr and Ala (TA-HSQC), as well as Asn and Gln (N-HSQC and QN-HSQC), are described. The new experiments are recorded as two-dimensional experiments and therefore need only small amounts of spectrometer time. The performance of the experiments is demonstrated with the application to two protein domains.

  7. The Origin of Nitrogen on Jupiter and Saturn from the $^{15}$N/$^{14}$N Ratio

    Fletcher, Leigh N; Orton, Glenn S; Irwin, Patrick G J; Mousis, Olivier; Sinclair, James A; Giles, Rohini S

    2014-01-01

    The Texas Echelon cross Echelle Spectrograph (TEXES), mounted on NASA's Infrared Telescope Facility (IRTF), was used to map mid-infrared ammonia absorption features on both Jupiter and Saturn in February 2013. Ammonia is the principle reservoir of nitrogen on the giant planets, and the ratio of isotopologues ($^{15}$N/$^{14}$N) can reveal insights into the molecular carrier (e.g., as N$_2$ or NH$_3$) of nitrogen to the forming protoplanets, and hence the source reservoirs from which these worlds accreted. We targeted two spectral intervals (900 and 960 cm$^{-1}$) that were relatively clear of terrestrial atmospheric contamination and contained close features of $^{14}$NH$_3$ and $^{15}$NH$_3$, allowing us to derive the ratio from a single spectrum without ambiguity due to radiometric calibration (the primary source of uncertainty in this study). We present the first ground-based determination of Jupiter's $^{15}$N/$^{14}$N ratio (in the range from $1.4\\times10^{-3}$ to $2.5\\times10^{-3}$), which is consistent...

  8. Methods of clinical chemistry and isotopic technique for investigation of the nitrogen metabolism in man using 15N

    The present manual is a catalogue of methods representing theoretical and practical aspects of application of the stable isotope 15N in medicine as well as a reference book for users of 15N techniques in life sciences. Special emphasis is given to the planning of 15N tracer experiments and their interpretation, sources of error and standard values of nitrogen compounds, information on sampling of medical materials, methods of separation and determination of proteins and non-protein nitrogen compounds in serum and urine, and details of the isotopic analysis of nitrogen by emission and mass spectrometry. (author)

  9. Distribution of /sup 15/N fertilizer in field-lysimeters sown with garlic (Allium sativum) and foxtail millet (Setaria italica)

    Lazzari, M.A. (Universidad Nacional del Sur, Bahia Blanca (Argentina). Dept. de Ciencas Agrarias)

    1982-01-01

    We examined the distribution of residual /sup 15/N and its uptake by a foxtail millet crop grown in field lysimeters following a previous garlic crop fertilized with either /sup 15/N-urea or /sup 15/N-ammonium sulphate. Garlic apparently removed more N from the lysimeters treated with urea-N than from those treated with (NH/sub 4/)/sub 2/SO/sub 4/. Fertilizer-N in the lysimeters was similar (ca. 32% of original) following millet harvest. About 16 per cent of both fertilizers in the lysimeters was removed by the millet.

  10. Medium-term effects of poultry manure on pine N uptake in a 15N labelled burnt soil.

    Castro, A; González Prieto, S. J.; T. Carballas

    2008-01-01

    The effects of poultry manure (PM), used for the reclamation of a 15N-labelled burnt soil, on N nutrition of pine seedlings were evaluated during a year in a pot experiment. Six treatments were used: 15N-labelled soil (LS), 15N-labelled burnt soil (BLS) and BLS+PM at doses equivalent to 1, 2, 4 and 8 Mg ha-1 of dry PM (PM1, PM2, PM4 and PM8, respectively). Either in the whole tree or the different organs, N concentration: a) decreased (P # 0.05) in the order LS > BLS, BLS+PM1, BLS...

  11. Determination of Nitrogen Uptake and Fertilizer Use Efficiency in Maize (Zea mays L.) Using the 15N Labeling Method

    There is an increasing concern for maximizing the efficiency of fertilizer nitrogen (N) use in crop production systems and the 15N techniques have been used extensively to study the uptake of applied N by plants and the nitrate concentration in soils at different depths. The 15N labeling method, the isotopic signature of the enriched tracer can be pre-determined to ensure significant difference in atom % of 15N between source and background level, even when fractionation occurs. This technique has been used extensively to trace fate of soil nitrate in cropping systems

  12. Distribution of 15N fertilizer in field-lysimeters sown with garlic (Allium sativum) and foxtail millet (Setaria italica)

    We examined the distribution of residual 15N and its uptake by a foxtail millet crop grown in field lysimeters following a previous garlic crop fertilized with either 15N-urea or 15N-ammonium sulphate. Garlic apparently removed more N from the lysimeters treated with urea-N than from those treated with (NH4)2SO4. Fertilizer-N in the lysimeters was similar (ca. 32% of original) following millet harvest. About 16 per cent of both fertilizers in the lysimeters was removed by the millet. (orig.)

  13. The Influence of Seed-borne N in 15N Isotope Dilution Studies with Legumes The Influence of Seed-borne N in 15N Isotope Dilution Studies with Legumes

    Jensen, Erik Steen; Andersen, A. J.; Thomsen, J. D.

    1985-01-01

    The distriution of seed-borne N in shoot and root of pea and field bean was studied using three methods: 1) determination of the N content in shoot and root of plants grown in sand culture without other N sources. 2) 15N isotope dilution in plants grown in Rhizobium-free medium supplied with 15N......-labelled nitrate and 3) determination of the 15N-enrichment in shoot and root of plants in which the seed-borne N was labelled with 15N. The results from the three methods were concordant, showing that from 44 to 50% of the seed-borne N in the two species was located in above-ground plant parts. The effect of...... corrections for seed-borne N in studies of nitrogen fixation in legumes is discussed....

  14. Dynamics of nitrogen in an oxic paleudalf soil with the incorporation of 15N-tagged organic nitrogen (maize straw) and 15N-tagged mineral nitrogen (ammonium sulphate)

    An experiment, carried out under field conditions in 12 lysimeters, each containing 3.0 ton of Oxic Paleudalf soil with four replicates, is described. This objective is labelling soil organic N. Nitrogen was incorporated into soil as maize straw, non-labelled and labelled with 15N and ammonium sulphate - 15N. The soil was sampled every 15 days in three different depths. N as NH+4, NO-3, total-N and (%)C and (%) moisture was analysed. (M.A.C.)

  15. 4-Oxalocrotonate tautomerase, a 41-kDa homohexamer: backbone and side-chain resonance assignments, solution secondary structure, and location of active site residues by heteronuclear NMR spectroscopy.

    Stivers, J T; Abeygunawardana, C; Whitman, C. P.; Mildvan, A. S.

    1996-01-01

    4-Oxalocrotonate tautomerase (4-OT), a homohexamer consisting of 62 residues per subunit, catalyzes the isomerization of unsaturated alpha-keto acids using Pro-1 as a general base (Stivers et al., 1996a, 1996b). We report the backbone and side-chain 1H, 15N, and 13C NMR assignments and the solution secondary structure for 4-OT using 2D and 3D homonuclear and heteronuclear NMR methods. The subunit secondary structure consists of an alpha-helix (residues 13-30), two beta-strands (beta 1, residu...

  16. Evaluation of Green Manures as Nitrogen Source for Maize Using 15N Labeling Technique

    The intensive and inappropriate use of soil for agricultural production aggravates the degradation of soil organic matter (SOM). Maintaining or even improving SOM is vital for sustaining the intensification of crop production in small farmer holdings. Application of green manures promotes changes in the soil chemical, physical and biological characteristics and improves soil fertility and quality. The effectiveness of green manures as a source of nutrients varies among species and cultivars and its integrated use with mineral fertilizer. Maize is one of the main no-tillage crops in Brazil, which is grown mainly in the savannah areas in rotation and/or succession with soybean and cotton crops. As N is required in large amounts for maize production, it is of great importance to know the capacity of green manures to supply N for its production. Field studies were carried out in Southern Cerrado (savannah), Brazil to evaluate the effectiveness of different nitrogen rates and green manures on maize productivity and to estimate the green manures 'N utilization by maize crop grown under a no-tillage system. Four green manures labeled with 15N that include sunnhemp (Crotalaria juncea L.), pigeon pea (Cajanus cajan L.), green velvet bean (Mucuna prurens), millet (Pennisetum glaucum L.) and spontaneous vegetation (fallow) combined with four N rates (0, 30, 90 and 150 kg ha-1) as urea, were tested for their contribution to N uptake by maize. The results from this field study showed that legume green manures (green velvet been and pigeon pea) provided more N to maize crop grown in sequence, compared to millet residues, in spite of larger amount of N in the millet residues, suggesting that residues of these two green manures favored soil conditions for N uptake. This may be due to its low C/N ratio leading to faster and regular release of N and other nutrients that are mineralized concomitantly to N. Millet, with high C/N ratio causing temporary immobilization of N, leads to a

  17. Reconstruction of the Sunspot Group Number: the Backbone Method

    Svalgaard, Leif

    2015-01-01

    We have reconstructed the sunspot group count, not by comparisons with other reconstructions and correcting those where they were deemed to be deficient, but by a re-assessment of original sources. The resulting series is a pure solar index and does not rely on input from other proxies, e.g. radionuclides, auroral sightings, or geomagnetic records. 'Backboning' the data sets, our chosen method, provides substance and rigidity by using long-time observers as a stiffness character. Solar activity, as defined by the Group Number, appears to reach and sustain for extended intervals of time the same level in each of the last three centuries since 1700 and the past several decades do not seem to have been exceptionally active, contrary to what is often claimed.

  18. Variation of protein backbone amide resonance by electrostatic field

    Sharley, John N

    2015-01-01

    Amide resonance is found to be sensitive to electrostatic field with component parallel or antiparallel the amide C-N bond. This effect is linear and without threshold in the biologically plausible electrostatic field range -0.005 to 0.005 au. Variation of amide resonance varies Resonance Assisted Hydrogen Bonding such as occurs in the hydrogen bonded chains of backbone amides of protein secondary structures such as beta sheet and non-polyproline helix such as alpha helix, varying the stability of the secondary structure. The electrostatic properties including permittivity of amino acid residue sidegroups influence the electrostatic field component parallel or antiparallel the C-N bond of each amide. The significance of this factor relative to other factors in protein folding depends on the magnitude of electrostatic field component parallel or antiparallel the C-N bond of each amide, and preliminary protein-scale calculations of the magnitude of these components suggest this factor warrants investigation in ...

  19. Design of an IPTV Multicast System for Internet Backbone Networks

    D. Gilbert

    2010-01-01

    Full Text Available The design of an IPTV multicast system for the Internet backbone network is presented and explored through extensive simulations. In the proposed system, a resource reservation algorithm such as RSVP, IntServ, or DiffServ is used to reserve resources (i.e., bandwidth and buffer space in each router in an IP multicast tree. Each router uses an Input-Queued, Output-Queued, or Crosspoint-Queued switch architecture with unity speedup. A recently proposed Recursive Fair Stochastic Matrix Decomposition algorithm used to compute near-perfect transmission schedules for each IP router. The IPTV traffic is shaped at the sources using Application-Specific Token Bucker Traffic Shapers, to limit the burstiness of incoming network traffic. The IPTV traffic is shaped at the destinations using Application-Specific Playback Queues, to remove residual network jitter and reconstruct the original bursty IPTV video streams at each destination. All IPTV traffic flows are regenerated at the destinations with essentially zero delay jitter and essentially-perfect QoS. The destination nodes deliver the IPTV streams to the ultimate end users using the same IPTV multicast system over a regional Metropolitan Area Network. It is shown that all IPTV traffic is delivered with essentially-perfect end-to-end QoS, with deterministic bounds on the maximum delay and jitter on each video frame. Detailed simulations of an IPTV distribution system, multicasting several hundred high-definition IPTV video streams over several essentially saturated IP backbone networks are presented.

  20. Nitrogen use efficiency evaluation of aerobic rice under field capacity water potential using 15N isotopic tracer technique

    Wahid, Ahmad Nazrul Abd; Rahim, Sahibin Abd; Rahim, Khairuddin Abdul; Harun, Abdul Rahim

    2015-09-01

    This study was carried out to evaluate the efficiency use of the nitrogen fertilizer on aerobic rice varieties MR219-4 and MR219-9 which were grown aerobically under field capacity water potential at the controlled environment area or shield house. Direct 15N isotope tracer method was used in this study, whereby the 15N isotope was utilized as a tracer for nitrogen nutrient uptake. 15N isotope presence in the samples is determined by using emission spectrometer analysis and percentage of total nitrogen is determined by using Kjeldahl method. 15N atom access value contained in the sample will be used in determining the effectiveness of the use of nitrogen in fertilizers through the specific calculation formulas. In this work, the data several data of nitrogen derived from fertilizer (Ndff), total nitrogen, nitrogen uptake and nitrogen use efficiency was obtained.

  1. 15N and 1H NMR evidence for multiple conformations of the complex of dihydrofolate reductase with its substrate, folate

    The binding of folate to Lactobacillus casei dihydrofolate reductase in the presence and absence of NADP+ has been studied by 15N NMR, using [5-15N]folate. In the presence of NADP+, three separate signals were observed for the single 15N atom, in agreement with our earlier evidence from 1H and 13C NMR for multiple conformations of this complex. The 15N spectra of the binary enzyme-folate complex provide evidence for the first time that this complex also exists in at least two conformational states. This is confirmed by the observation of two separate resonances for the 7-proton of bound folate, located by two-dimensional exchange spectroscopy. 15 refs.; 3 figs.; 1 table

  2. Nitrogen use efficiency evaluation of aerobic rice under field capacity water potential using {sup 15}N isotopic tracer technique

    Wahid, Ahmad Nazrul Abd, E-mail: a-nazrul@nuclearmalaysia.gov.my [Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, 43600, Selangor (Malaysia); Malaysian Nuclear Agency, Bangi, 43000 Kajang, Selangor (Malaysia); Rahim, Sahibin Abd, E-mail: haiyan@ukm.edu.my [Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, 43600, Selangor (Malaysia); Rahim, Khairuddin Abdul; Harun, Abdul Rahim [Malaysian Nuclear Agency, Bangi, 43000 Kajang, Selangor (Malaysia)

    2015-09-25

    This study was carried out to evaluate the efficiency use of the nitrogen fertilizer on aerobic rice varieties MR219-4 and MR219-9 which were grown aerobically under field capacity water potential at the controlled environment area or shield house. Direct {sup 15}N isotope tracer method was used in this study, whereby the {sup 15}N isotope was utilized as a tracer for nitrogen nutrient uptake. {sup 15}N isotope presence in the samples is determined by using emission spectrometer analysis and percentage of total nitrogen is determined by using Kjeldahl method. {sup 15}N atom access value contained in the sample will be used in determining the effectiveness of the use of nitrogen in fertilizers through the specific calculation formulas. In this work, the data several data of nitrogen derived from fertilizer (Ndff), total nitrogen, nitrogen uptake and nitrogen use efficiency was obtained.

  3. Nitrogen use efficiency evaluation of aerobic rice under field capacity water potential using 15N isotopic tracer technique

    This study was carried out to evaluate the efficiency use of the nitrogen fertilizer on aerobic rice varieties MR219-4 and MR219-9 which were grown aerobically under field capacity water potential at the controlled environment area or shield house. Direct 15N isotope tracer method was used in this study, whereby the 15N isotope was utilized as a tracer for nitrogen nutrient uptake. 15N isotope presence in the samples is determined by using emission spectrometer analysis and percentage of total nitrogen is determined by using Kjeldahl method. 15N atom access value contained in the sample will be used in determining the effectiveness of the use of nitrogen in fertilizers through the specific calculation formulas. In this work, the data several data of nitrogen derived from fertilizer (Ndff), total nitrogen, nitrogen uptake and nitrogen use efficiency was obtained

  4. 15N isotope biogeochemistry and natural denitrification process in groundwater: Application to the chalk aquifer of norther France

    The use of 15N natural isotope tracing in an aquifer contained within chalk rocks in northern France indicates that, under certain hydrogeological conditions, major denitrification occurs. At the boundary where the aquifer becomes confined, the nitrate concentrations decrease in the direction of groundwater flow accompanied by an exponential increase in 15N (expressed in δ15N) of the residual nitrate. This is characteristic of kinetic isotope effects, which accompany the reduction of the nitrate ion during denitrification. Hydrogeochemical and bacteriological observations confirm this process. Natural isotope tracing also permits this process to be distinguished from local dilution with nitrate-free water, which would entail a major drop in nitrate values without 15N isotopic enrichment. A model is proposed to explain the relatively small observed magnitude of the isotopic fractionation effect

  5. Cavity ring-down spectroscopy of the 6ν3 bands of 15N substituted N2O

    The 6ν3 and ν2+6ν3-ν2 bands of 15N substituted nitrous oxide isotopologues have been recorded by a continuous-wave cavity ring-down spectrometer (CW-CRDS) operated near 0.8μm. The sensitivity limit was at the level of 1x10-10/cm. In total, 213, 86 and 191 transitions were observed for the 14N15N16O, 15N14N16O and 15N216O isotopologues, respectively. The ro-vibrational spectroscopic parameters of the upper states are determined from least square fitting of the transitions. The absolute line intensities of the 6ν3 cold bands have been retrieved by a multi-line fitting procedure from the spectra with an estimated accuracy of 4% for majority of the unblended lines. The vibrational transition dipole moment squared values and the empirical Herman-Wallis coefficients are also presented.

  6. An optimized method for {sup 15}N R{sub 1} relaxation rate measurements in non-deuterated proteins

    Gairí, Margarida, E-mail: mgairi@rmn.ub.edu [University of Barcelona (CCiTUB), NMR Facility, Scientific and Technological Centers (Spain); Dyachenko, Andrey [Institute for Research in Biomedicine (IRB) (Spain); González, M. Teresa; Feliz, Miguel [University of Barcelona (CCiTUB), NMR Facility, Scientific and Technological Centers (Spain); Pons, Miquel [University of Barcelona, Biomolecular NMR Laboratory and Organic Chemistry Department (Spain); Giralt, Ernest, E-mail: ernest.giralt@irbbarcelona.org [Institute for Research in Biomedicine (IRB) (Spain)

    2015-06-15

    {sup 15}N longitudinal relaxation rates are extensively used for the characterization of protein dynamics; however, their accurate measurement is hindered by systematic errors. {sup 15}N CSA/{sup 1}H–{sup 15}N dipolar cross-correlated relaxation (CC) and amide proton exchange saturation transfer from water protons are the two main sources of systematic errors in the determination of {sup 15}N R{sub 1} rates through {sup 1}H–{sup 15}N HSQC-based experiments. CC is usually suppressed through a train of 180° proton pulses applied during the variable {sup 15}N relaxation period (T), which can perturb water magnetization. Thus CC cancellation is required in such a way as to minimize water saturation effects. Here we examined the level of water saturation during the T period caused by various types of inversion proton pulses to suppress CC: (I) amide-selective IBURP-2; (II) cosine-modulated IBURP-2; (III) Watergate-like blocks; and (IV) non-selective hard. We additionally demonstrate the effect of uncontrolled saturation of aliphatic protons on {sup 15}N R{sub 1} rates. In this paper we present an optimized pulse sequence that takes into account the crucial effect of controlling also the saturation of the aliphatic protons during {sup 15}N R{sub 1} measurements in non-deuterated proteins. We show that using cosine-modulated IBURP-2 pulses spaced 40 ms to cancel CC in this optimized pulse program is the method of choice to minimize systematic errors coming from water and aliphatic protons saturation effects.

  7. Synthesis and optical resolution of the neurotoxin 2-amino-3-([[sup 15]N]-methylamino)propanoic acid (BMAA)

    Yulin Hu; Ziffer, H. (National Inst. of Diabetes and Digestive and Kidney Diseases, Bethesda, MD (United States))

    1990-05-01

    The synthesis of 2-amino-3-([[sup 15]N]-methylamino)propanoic acid (synonyms, BMAA, [beta]-N-mehylamino-alanine) from [alpha]-acetamidoacrylic acid and [[sup 15]N]-methylamine is described. Enantioselective hydrolysis of the acetamide group, mediated by the enzyme Acylase 1 (EC 3.5.1.14), yielded (R)-BMAA and the (S)-[alpha]-acetamido derivative. Acid hydrolysis of the latter compound yielded (S)-BMAA. (author).

  8. Natural and artificial methods of 15N labelling of soil to estimate biological nitrogen fixation: Review of symposium papers

    Despite the many criticisms that have sometimes tended to limit confidence in the 15N methodologies, papers have been presented at the symposium to show the practical importance of the 15N methods, how to reduce postulated errors, and when errors due to reference crops can be ignored. Besides, in many situations, the required answers can be obtained without the need for a reference crop. (author). 21 refs

  9. Species specific and environment induced variation of δ(13)C and δ(15)N in alpine plants.

    Yang, Yang; Siegwolf, Rolf T W; Körner, Christian

    2015-01-01

    Stable carbon and nitrogen isotope signals in plant tissues integrate plant-environment interactions over long periods. In this study, we hypothesized that humid alpine life conditions are narrowing the scope for significant deviations from common carbon, water and nitrogen relations as captured by stable isotope signals. We explored the variation in δ(13)C and δ(15)N in 32 plant species from tissue type to ecosystem scale across a suite of locations at c. Two thousand five hundred meter elevation in the Swiss Alps. Foliar δ(13)C and δ(15)N varied among species by about 3-4‰ and 7-8‰ respectively. However, there was no overall difference in means of δ(13)C and δ(15)N for species sampled in different plant communities or when bulk plant dry matter harvests of different plant communities were compared. δ(13)C was found to be highly species specific, so that the ranking among species was mostly maintained across 11 habitats. However, δ(15)N varied significantly from place to place in all species (a range of 2.7‰) except in Fabaceae (Trifolium alpinum) and Juncaceae (Luzula lutea). There was also a substantial variation among individuals of the same species collected next to each other. No difference was found in foliar δ(15)N of non-legumes, which were either collected next to or away from the most common legume, T. alpinum. δ(15)N data place Cyperaceae and Juncaceae, just like Fabaceae, in a low discrimination category, well separated from other families. Soil δ(15)N was higher than in plants and increased with soil depth. The results indicate a high functional diversity in alpine plants that is similar to that reported for low elevation plants. We conclude that the surprisingly high variation in δ(13)C and δ(15)N signals in the studied high elevation plants is largely species specific (genetic) and insensitive to obvious environmental cues. PMID:26097487

  10. Variability in δ15N of intertidal brown algae along a salinity gradient: Differential impact of nitrogen sources

    While it is generally agreed that δ15N of brown macroalgae can discriminate between anthropogenic and natural sources of nitrogen, this study provides new insights on net fractionation processes occurring in some of these species. The contribution of continental and marine sources of nitrogen to benthic macroalgae in the estuary-ria system of A Coruña (NW Spain) was investigated by analyzing the temporal (at a monthly and annual basis) and spatial (up to 10 km) variability of δ15N in the macroalgae Ascophyllum nodosum and three species of the genus Fucus (F. serratus, F. spiralis and F. vesiculosus). Total nitrate and ammonium concentrations and δ15N-DIN, along with salinity and temperature in seawater were also studied to address the sources of such variability. Macroalgal δ15N and nutrient concentrations decreased from estuarine to marine waters, suggesting larger dominance of anthropogenic nitrogen sources in the estuary. However, δ15N values of macroalgae were generally higher than those of ambient nitrogen at all temporal and spatial scales considered. This suggests that the isotopic composition of these macroalgae is strongly affected by fractionation during uptake, assimilation or release of nitrogen. The absence of correlation between macroalgal and water samples suggests that the δ15N of the species considered cannot be used for monitoring short-term changes. But their long lifespan and slow turnover rates make them suitable to determine the impact of the different nitrogen sources integrated over long-time periods. - Highlights: • Variability of Fucacean δ15N indicates N sources along a salinity gradient. • δ15N of Fucaceae and seawater are not correlated at short time scales. • Isotopic fractionation in macroalgal tissue varies at seasonal and at local scale. • Fucacean species are suitable for monitoring chronic N loadings

  11. Synthesis and optical resolution of the neurotoxin 2-amino-3-([15N]-methylamino)propanoic acid (BMAA)

    The synthesis of 2-amino-3-([15N]-methylamino)propanoic acid (synonyms, BMAA, β-N-mehylamino-alanine) from α-acetamidoacrylic acid and [15N]-methylamine is described. Enantioselective hydrolysis of the acetamide group, mediated by the enzyme Acylase 1 (EC 3.5.1.14), yielded (R)-BMAA and the (S)-α-acetamido derivative. Acid hydrolysis of the latter compound yielded (S)-BMAA. (author)

  12. Variability in δ{sup 15}N of intertidal brown algae along a salinity gradient: Differential impact of nitrogen sources

    Viana, Inés G., E-mail: inesgviana@gmail.com; Bode, Antonio

    2015-04-15

    While it is generally agreed that δ{sup 15}N of brown macroalgae can discriminate between anthropogenic and natural sources of nitrogen, this study provides new insights on net fractionation processes occurring in some of these species. The contribution of continental and marine sources of nitrogen to benthic macroalgae in the estuary-ria system of A Coruña (NW Spain) was investigated by analyzing the temporal (at a monthly and annual basis) and spatial (up to 10 km) variability of δ{sup 15}N in the macroalgae Ascophyllum nodosum and three species of the genus Fucus (F. serratus, F. spiralis and F. vesiculosus). Total nitrate and ammonium concentrations and δ{sup 15}N-DIN, along with salinity and temperature in seawater were also studied to address the sources of such variability. Macroalgal δ{sup 15}N and nutrient concentrations decreased from estuarine to marine waters, suggesting larger dominance of anthropogenic nitrogen sources in the estuary. However, δ{sup 15}N values of macroalgae were generally higher than those of ambient nitrogen at all temporal and spatial scales considered. This suggests that the isotopic composition of these macroalgae is strongly affected by fractionation during uptake, assimilation or release of nitrogen. The absence of correlation between macroalgal and water samples suggests that the δ{sup 15}N of the species considered cannot be used for monitoring short-term changes. But their long lifespan and slow turnover rates make them suitable to determine the impact of the different nitrogen sources integrated over long-time periods. - Highlights: • Variability of Fucacean δ{sup 15}N indicates N sources along a salinity gradient. • δ{sup 15}N of Fucaceae and seawater are not correlated at short time scales. • Isotopic fractionation in macroalgal tissue varies at seasonal and at local scale. • Fucacean species are suitable for monitoring chronic N loadings.

  13. 15N nuclear reaction analysis for hydrogen profiling at TIT 4.75 MV Van de Graaff

    A 15N beam line has been upgraded by installing a new analyzing magnet and by controlling beam parameters with a computer. An improved beam intensity of ∼ 20 pnA has realized a detection sensitivity of 1020 H · cm-3 in the hydrogen profilling. The hydrogen profiles have been measured by the 15N nuclear reaction for TiHx and TiHx-Au samples. These profiles are compared with the profiles obtained by SIMS. (author)

  14. An Unusual Conformational Isomer of Verrucosidin Backbone from a Hydrothermal Vent Fungus, Penicillium sp. Y-50-10.

    Pan, Chengqian; Shi, Yutong; Auckloo, Bibi Nazia; Chen, Xuegang; Chen, Chen-Tung Arthur; Tao, Xinyi; Wu, Bin

    2016-01-01

    A new verrucosidin derivative, methyl isoverrucosidinol (1), was isolated from the marine fungus Penicillium sp. Y-50-10, dwelling in sulfur rich sediment in the Kueishantao hydrothermal vents off Taiwan. The structure was established by spectroscopic means including HRMS and 2D-NMR spectroscopic analysis. The absolute configuration was defined mainly by comparison of quantum chemical TDDFT calculated and experimental ECD spectra. Among hitherto known compounds with a verrucosidine backbone isolated from natural resource, compound 1 represents the first example of a new conformational isomer of its skeleton, exhibiting antibiotic activity against Bacillus subtilis with MIC value 32 μg/mL. PMID:27548192

  15. An Unusual Conformational Isomer of Verrucosidin Backbone from a Hydrothermal Vent Fungus, Penicillium sp. Y-50-10

    Chengqian Pan

    2016-08-01

    Full Text Available A new verrucosidin derivative, methyl isoverrucosidinol (1, was isolated from the marine fungus Penicillium sp. Y-50-10, dwelling in sulfur rich sediment in the Kueishantao hydrothermal vents off Taiwan. The structure was established by spectroscopic means including HRMS and 2D-NMR spectroscopic analysis. The absolute configuration was defined mainly by comparison of quantum chemical TDDFT calculated and experimental ECD spectra. Among hitherto known compounds with a verrucosidine backbone isolated from natural resource, compound 1 represents the first example of a new conformational isomer of its skeleton, exhibiting antibiotic activity against Bacillus subtilis with MIC value 32 μg/mL.

  16. Effects of Tryptophan Content and Backbone Spacing on the Uptake Efficiency of Cell-Penetrating Peptides

    Rydberg, Hanna A.

    2012-07-10

    Cell-penetrating peptides (CPPs) are able to traverse cellular membranes and deliver macromolecular cargo. Uptake occurs through both endocytotic and nonendocytotic pathways, but the molecular requirements for efficient internalization are not fully understood. Here we investigate how the presence of tryptophans and their position within an oligoarginine influence uptake mechanism and efficiency. Flow cytometry and confocal fluorescence imaging are used to estimate uptake efficiency, intracellular distribution and toxicity in Chinese hamster ovarian cells. Further, membrane leakage and lipid membrane affinity are investigated. The peptides contain eight arginine residues and one to four tryptophans, the tryptophans positioned either at the N-terminus, in the middle, or evenly distributed along the amino acid sequence. Our data show that the intracellular distribution varies among peptides with different tryptophan content and backbone spacing. Uptake efficiency is higher for the peptides with four tryptophans in the middle, or evenly distributed along the peptide sequence, than for the peptide with four tryptophans at the N-terminus. All peptides display low cytotoxicity except for the one with four tryptophans at the N-terminus, which was moderately toxic. This finding is consistent with their inability to induce efficient leakage of dye from lipid vesicles. All peptides have comparable affinities for lipid vesicles, showing that lipid binding is not a decisive parameter for uptake. Our results indicate that tryptophan content and backbone spacing can affect both the CPP uptake efficiency and the CPP uptake mechanism. The low cytotoxicity of these peptides and the possibilities of tuning their uptake mechanism are interesting from a therapeutic point of view. © 2012 American Chemical Society.

  17. Creating 13C- and 15N-enriched tree leaf litter for decomposition experiments

    Szlavecz, K. A.; Pitz, S.; Chang, C.; Bernard, M.

    2013-12-01

    Labeling plant material with heavy isotopes of carbon and nitrogen can produce a traceable nutrient signal that can be followed into the different trophic levels and decomposer food web. We treated 60 tree saplings with 13C-enriched CO2 gas and 15N-enriched ammonium nitrate over a three-month period to create dually-labeled plant material for future decomposition experiments. The trees included both early (Red maple, Sweetgum, Tulip poplar) and late (American beech, White oak) successional deciduous tree species, and a conifer, White pine. We constructed a 2.4 m × 2.4 m × 2.4 m environmental chamber that was climate-controlled using an air conditioning system. An Arduino microcontroller interfaced with a Vaisala GMP343 CO2 probe maintained a CO2 concentration between 500-520 ppm by controlling a solenoid valve on the CO2 tank regulator. The trees were placed into the chamber in August 2012 and remained until senescence unless they were lost to death or disease. Ammonium nitrate was added twice, in September and October. Leaf samples were collected prior to the start of the experiment and after senescence, whereas root samples were collected only in December. Samples were dried, ground and analyzed using an isotope ratio mass spectrometer. American beech and White oak had 40% mortality, and 34% of tulip poplar trees were removed because of powdery mildew overgrowth or death. Most tulip poplar trees exhibited a second leaf out following senescence in late September. Nearly 1 kg of litter was produced with tulip poplar representing over half of the total mass. Levels of enrichment varied greatly by species. Beech (-14.2‰) and White oak (-4.8‰) had low levels of enrichment in comparison to early successional species such as Sweetgum (41.7‰) and Tulip poplar (30.7‰ [first leaf fall] and 238.0‰ [second leaf fall]). Leaf enrichment with 15N followed a similar pattern, though it was achieved at a higher level with δ15N values varying from 271.6‰ to 1354.2

  18. Measurement of denitrification on grassland using gas chromatography and 15N tracer technique

    Alternative covering of grassland micro-plots fertilized with 15NH415NO3 allowed on the basis on N2 and N2O quantities released within several weeks to measure denitrification and to calculate it by means of methane as gas tracer. Thus the gas exchange was rendered visible and the N quantities measured could be corrected. In some variants, the acetylene blocking technique was successfully applied by adding acetylene to the soil air. The losses measured at 6 dates are discussed together with the 15N balance and atmospherical conditions. The method is suited for recording the high losses occurring mainly in the second quarter of the year immediately after fertilization. Under the conditions mentioned soil N losses were small (3 kg N/ha). The immobilized fertilizer N quantities reached 20 to 30 kg/ha (fertilizer rate 100 kg N/ha) and were comparably independent of the date of fertilization. (author)

  19. Potential denitrification in arable soil samples at winter temperatures - measurements by 15N gas analysis

    In samples from the plough horizon of five soils taken after cereal harvest, denitrification was measured as volatilization of N2 and N2O from 15N nitrate in the absence of O2. Nitrate contents lower than 50 ppm N (related to soil dry matter) had only a small effect on denitrification velocity in four of the five soils. In a clay soil dependence on nitrate concentration corresponded to a first-order reaction. Available C was no limiting factor. Even at zero temperatures remarkable N amounts (on average 0.2 ppm N per day) were still denitrified. The addition of daily turnover rates in relation to soil temperatures prevailing from December to March revealed potential turnovers in the 0-to-30-cm layer of the soils to average 28 ± 5 ppm N. (author)

  20. 1H, 13C, and 15N resonance assignments of murine amelogenin, an enamel biomineralization protein.

    Buchko, Garry W.; Bekhazi, Jacky G.; Cort, John R.; Valentine, Nancy B.; Snead, Malcolm L.; Shaw, Wendy J.

    2008-06-01

    Amelogenin is the predominant matrix protein in developing dental enamel. Making extensive use of residue-specific 15N-labeled amino acids samples, the majority of the main and side chain resonances for murine amelogenin were assigned in 2% aqueous acetic acid at pH 3.0. This research was performed at Pacific Northwest National Laboratory, operated by Battelle for the US-DOE. A large part of this research was performed at the W.R. Wiley Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by U.S. Department of Energy’s Office of Biological and Environmental Research (BER) program located at Pacific Northwest National Laboratory (PNNL).

  1. A 15N investigation of mineral fertilizer nitrogen assimilation in apples

    An experiment was made using six seedlings of the apple cv. Golden Delicious in their second year of growing. The roots of each seedling were divided and planted in two vegetation pots of 1 l capacity. Fertilizer application of 1 g NH4NO3 with 49.1 atom % 15N was effected to three of the plants in one of the pots, while to the remaining three plants in both pots the fertilizer application consisted of 0.5 g 15NH4NO3 for each pot. Isotope analysis of fertilizer N taken up was made and the coefficient of its assimilation was determined. Twenty-one days later the plants had assimilated 18.18-21.95% of the mineral N applied. This amount constituted 17.32-22.13% of the total N assimilated. The percent of assimilation was higher in case the fertilizer was applied to both pots

  2. Fate of nitrogen fertilizers labelled with 15 N in two soil samples of Central Amazon, Brazil

    The efficiency of two nitrogen fertilizers, ammonium sulphate and urea, labelled with 15 N, in two major Central-Amazonian soils (Yellow Latosol an Oxisol and Red-Yellow Podzolic - an Ultisol), was studied in greenhouse experiments in Nancy, France, 1992. Italian rye-grass (Lolium multiflorum L.) was used as the test plant. Rye-grass nitrogen uptake of ammonium sulphate ranged from 44 tp 49%, and of urea from 60 to 70%. Immobilization and losses of nitrogen were dependent on the fertilizer type. Microbial nitrogen immobilization was higher in the presence of urea, while losses were higher with ammonium sulphate. Since losses of nitrogen fertilizers from leaching were practically nil under the experimental conditions, they might have occurred mainly through gaseous form. (author)

  3. Nuclear Quadrupole Hyperfine Structure in HC14N/H14NC and DC15N/D15NC Isomerization: A Diagnostic Tool for Characterizing Vibrational Localization

    Wong, Bryan M

    2010-01-01

    Large-amplitude molecular motions which occur during isomerization can cause significant changes in electronic structure. These variations in electronic properties can be used to identify vibrationally-excited eigenstates which are localized along the potential energy surface. This work demonstrates that nuclear quadrupole hyperfine interactions can be used as a diagnostic marker of progress along the isomerization path in both the HC14N/H14NC and DC15N/D15NC chemical systems. Ab initio calculations at the CCSD(T)/cc-pCVQZ level indicate that the hyperfine interaction is extremely sensitive to the chemical bonding of the quadrupolar 14N nucleus and can therefore be used to determine in which potential well the vibrational wavefunction is localized. A natural bonding orbital analysis along the isomerization path further demonstrates that hyperfine interactions arise from the asphericity of the electron density at the quadrupolar nucleus. Using the CCSD(T) potential surface, the quadrupole coupling constants of...

  4. Correlation between the synthetic origin of methamphetamine samples and their {sup 15}N and {sup 13}C stable isotope ratios

    Billault, Isabelle [Laboratoire d' Analyse Isotopique et Electrochimique de Metabolismes, CNRS UMR6006, University of Nantes, BP 92208, 44322 Nantes (France)]. E-mail: Isabelle.Billault@univ-nantes.fr; Courant, Frederique [Laboratoire d' Analyse Isotopique et Electrochimique de Metabolismes, CNRS UMR6006, University of Nantes, BP 92208, 44322 Nantes (France); Pasquereau, Leo [Laboratoire d' Analyse Isotopique et Electrochimique de Metabolismes, CNRS UMR6006, University of Nantes, BP 92208, 44322 Nantes (France); Derrien, Solene [Laboratoire d' Analyse Isotopique et Electrochimique de Metabolismes, CNRS UMR6006, University of Nantes, BP 92208, 44322 Nantes (France); Robins, Richard J. [Laboratoire d' Analyse Isotopique et Electrochimique de Metabolismes, CNRS UMR6006, University of Nantes, BP 92208, 44322 Nantes (France); Naulet, Norbert [Laboratoire d' Analyse Isotopique et Electrochimique de Metabolismes, CNRS UMR6006, University of Nantes, BP 92208, 44322 Nantes (France)

    2007-06-12

    The active ingredient of ecstasy, N-methyl-3,4-methyldioxyphenylisopropylamine (MDMA) can be manufactured by a number of easy routes from simple precursors. We have synthesised 45 samples of MDMA following the five most common routes using N-precursors from 12 different origins and three different precursors for the aromatic moiety. The {sup 13}C and {sup 15}N contents of both the precursors and the MDMA samples derived therefrom were measured by isotope ratio mass spectrometry coupled to an elemental analyser (EA-IRMS). We show that within-pathway correlation between the {sup 15}N content of the precursor and that of the derived MDMA can be strong but that no general pattern of correlation can be defined. Rather, it is evident that the {delta} {sup 15}N values of MDMA are strongly influenced by a combination of the {delta} {sup 15}N values of the source of nitrogen used, the route by which the MDMA is synthesised, and the experimental conditions employed. Multivariate analysis (PCA) based on the {delta} {sup 15}N values of the synthetic MDMA and of the {delta} {sup 15}N and {delta} {sup 13}C values of the N-precursors leads to good discrimination between the majority of the reaction conditions tested.

  5. Single Particle Strengths and Mirror States in $^{15}$N$-^{15}$O below 12.0 MeV

    Mertin, C E; Crisp, A M; Keeley, N; Kemper, K W; Momtyuk, O; Roeder, B T; Volya, A

    2014-01-01

    New $^{14}$N(d,p) angular distribution data were taken at a deuteron bombarding energy of 16 MeV to locate all narrow single particle neutron states up to 15 MeV in excitation. A new shell model calculation is able to reproduce all levels in $^{15}$N up to 11.5 MeV and is used to characterize a narrow single particle level at 11.236 MeV and to provide a map of the single particle strengths. The known levels in $^{15}$N are then used to determine their mirrors in the lesser known nucleus $^{15}$O. The 2s$_{1/2}$ and 1d$_{5/2}$ single particle centroid energies are determined for the $^{15}$N$-^{15}$O mirror pair as: $^{15}$N $(\\text{2s}_{1/2}) = 8.08$ MeV, $^{15}$O $(\\text{2s}_{1/2}) = 7.43$ MeV, $^{15}$N $(\\text{1d}_{5/2}) = 7.97$ MeV, and $^{15}$O $(\\text{1d}_{5/2}) = 7.47$ MeV. These results confirm the degeneracy of these orbits and that the $^{15}$N$-^{15}$O nuclei are where the transition between the $\\text{2s}_{1/2}$ lying below the $\\text{1d}_{5/2}$ to lying above it, takes place. The $\\text{1d}_{3/2}$...

  6. Cryptic or day-to-day parts of the riverbed N cycle - new challenges for 15N

    Trimmer, Mark; Ouyang, Liao; Lansdown, Katrina

    2016-04-01

    The discovery of anaerobic ammonium oxidation (anammox) not only changed our understanding of the nitrogen cycle in aquatic ecosystems but it also undermined some of the key 15N techniques used to study it. Reformulations of principle equations and the development of new 15N2 and 15N2O techniques enabled the simultaneous quantification of N2 production by anammox and denitrification in mainly soft, cohesive sediments where redox gradients are clearly defined and solute exchanged governed by diffusion. At the heart of the application of 15N, for the quantification of natural 14N cycling, is the key assumption that the respective pools of 15N and 14N are evenly mixed and that both are cycled without bias towards each other. Recent evidence, however, from a variety of aquatic ecosystems, suggests that this may not be the case. For example, organic N may be oxidised directly to N2 gas without ever mixing with the inorganic pool or inorganic intermediates (e.g. nitrite) are 'shunted' internally and also fail to mix evenly with the applied tracer pool. Our most recent work in permeable, oxic gravel riverbeds presents some particular challenges to the application of 15N. In these systems, a tight coupling between aerobic nitrification and anaerobic N2 production - in the presence of 100

  7. Investigating patterns of symbiotic nitrogen fixation during vegetation change from grassland to woodland using fine scale δ(15) N measurements.

    Soper, Fiona M; Boutton, Thomas W; Sparks, Jed P

    2015-01-01

    Biological nitrogen fixation (BNF) in woody plants is often investigated using foliar measurements of δ(15) N and is of particular interest in ecosystems experiencing increases in BNF due to woody plant encroachment. We sampled δ(15) N along the entire N uptake pathway including soil solution, xylem sap and foliage to (1) test assumptions inherent to the use of foliar δ(15) N as a proxy for BNF; (2) determine whether seasonal divergences occur between δ(15) Nxylem sap and δ(15) Nsoil inorganic N that could be used to infer variation in BNF; and (3) assess patterns of δ(15) N with tree age as indicators of shifting BNF or N cycling. Measurements of woody N-fixing Prosopis glandulosa and paired reference non-fixing Zanthoxylum fagara at three seasonal time points showed that δ(15) Nsoil inorganic N varied temporally and spatially between species. Fractionation between xylem and foliar δ(15) N was consistently opposite in direction between species and varied on average by 2.4‰. Accounting for these sources of variation caused percent nitrogen derived from fixation values for Prosopis to vary by up to ∼70%. Soil-xylem δ(15) N separation varied temporally and increased with Prosopis age, suggesting seasonal variation in N cycling and BNF and potential long-term increases in BNF not apparent through foliar sampling alone. PMID:24890575

  8. Rate of [15N] leucine incorporation and determination of nitrogenous fractions from gastro-jejunal secretion in fasting humans

    The aim of this study was to quantify the nitrogen fraction flow rates in gastro-jejunal secretions in fasting humans and to determine the [15N] leucine incorporation into the secreted proteins. A double lumen intestinal perfusion method was used in 5 healthy volunteers. Plasma and gastro-jejunal juices were collected during a 15-h intravenous [15N] leucine infusion. Total, soluble and insoluble nitrogen, amino acids and [15N] leucine enrichment were measured. The total nitrogen flow rate was 7.2 ± 1.9 mmol.h-1 and 58% was ethanol soluble. The amino-acid composition remained constant and glycine was the most abundant. The plasma [15N] leucine enrichment at the isotopic plateau was 4.8 ± 0.9 mol% excess. The [15N] leucine enrichment in the intestinal chyme increased asymptotically to reach a plateau after 5h. The [15N] leucine enrichment at the plateau and the fractional synthesis rate of secreted proteins were 1.6 ±0.5 mol% excess and 21.5 ± 3.3% h-1, respectively. These results show that the composition of the basal gastro-jejunal secretion is very stable. A part of this secretion is composed of proteins with rapid synthesis rates. (authors). 33 refs., 4 figs., 2 tabs

  9. 15N and 13C abundances in marine environments with emphasis on biogeochemical structure of food networks

    Distributions of δ15N and δ13C for biogenic substances in the Antarctic Ocean and in the Otsuchi River estuary in Japan were investigated to construct isotope biogeochemical framework for assessing marine ecosystems. The isotopic compositions of phytoplankton were particularly low in the Antarctic Ocean. High nitrate and CO2 concentrations in the surface sea waters, and the low light intensity seem to enhance the kinetic isotope fractionations that preferred the depletion of 15N and 13C in the algal body. A clear-cut linear relationship between animal δ15N and its trophic level was obtained in the Antarctic system. In the estuary, the variation of isotope ratios were principally governed by the mixing of land-derived organic matter, marine phytoplankton, and seagrasses. A food-chain effect of 15N enrichment was also confirmed. An isotopically ordered structure was presented for a marine estuarine ecosystem. The isotopic abundances in a food network vary mainly because of the variation in 15N and 13C contents of primary producers grown under different environmental conditions and because of the enrichment of 15N along food chains. (author)

  10. Cyanobacteria-derived nitrogen uptake by benthic invertebrates in Lake Taihu: a mesocosm study using 15N labeling

    Yu J.

    2014-01-01

    Full Text Available Eutrophication of lakes can lead to dominance by cyanobacteria, which are hardly used by zooplankton due to their low nutrition value. However, sedimented cyanobacterial detritus may be a useful source for benthic invertebrates. We studied the Microcystis-derived nitrogen incorporation in benthic invertebrates in Lake Taihu using stable isotopic nitrogen (15N as a tracer. The δ15N of all organisms increased significantly with time after addition of the labeled Microcystis detritus. δ15N values of POM and periphyton peaked earlier than for benthic invertebrates, and the maximum levels were also higher than bivalves, snails and worms (Limnodrilus spp.. Among benthic invertebrates, Radix swinhoei peaked later than other invertebrates, but the maximum level and the excess 15N of the last sampling day were higher. At the end of the experiment, approximately 70% of the added 15N was retained in the benthic food web, while only a small fraction (less than 1% of the added detritus 15N occurred in the pelagic food web. Our results suggest that nitrogen from cyanobacteria can be incorporated more in benthic than pelagic food webs and cyanobacterial blooms may contribute to the development of benthic animals.

  11. 15N/14N variations in Cretaceous Atlantic sedimentary sequences: implication for past changes in marine nitrogen biogeochemistry

    Rau, G.H.; Arthur, M.A.; Dean, W.E.

    1987-01-01

    At two locations in the Atlantic Ocean (DSDP Sites 367 and 530) early to middle Cretaceous organic-carbon-rich beds ("black shales") were found to have significantly lower ??15N values (lower 15N/14N ratios) than adjacent organic-carbon-poor beds (white limestones or green claystones). While these lithologies are of marine origin, the black strata in particular have ??15N values that are significantly lower than those previously found in the marine sediment record and most contemporary marine nitrogen pools. In contrast, black, organic-carbon-rich beds at a third site (DSDP Site 603) contain predominantly terrestrial organic matter and have C- and N-isotopic compositions similar to organic matter of modern terrestrial origin. The recurring 15N depletion in the marine-derived Cretaceous sequences prove that the nitrogen they contain is the end result of an episodic and atypical biogeochemistry. Existing isotopic and other data indicate that the low 15N relative abundance is the consequence of pelagic rather than post-depositional processes. Reduced ocean circulation, increased denitrification, and, hence, reduced euphotic zone nitrate availability may have led to Cretaceous phytoplankton assemblages that were periodically dominated by N2-fixing blue-green algae, a possible source of this sediment 15N-depletion. Lack of parallel isotopic shifts in Cretaceous terrestrially-derived nitrogen (Site 603) argues that the above change in nitrogen cycling during this period did not extend beyond the marine environment. ?? 1987.

  12. Rapid mass spectrometric analysis of 15N-Leu incorporation fidelity during preparation of specifically labeled NMR samples

    Truhlar, Stephanie M.E.; Cervantes, Carla F.; Torpey, Justin W.; Kjaergaard, Magnus; Komives, Elizabeth A.

    2008-01-01

    Advances in NMR spectroscopy have enabled the study of larger proteins that typically have significant overlap in their spectra. Specific 15N-amino acid incorporation is a powerful tool for reducing spectral overlap and attaining reliable sequential assignments. However, scrambling of the label during protein expression is a common problem. We describe a rapid method to evaluate the fidelity of specific 15N-amino acid incorporation. The selectively labeled protein is proteolyzed, and the resulting peptides are analyzed using MALDI mass spectrometry. The 15N incorporation is determined by analyzing the isotopic abundance of the peptides in the mass spectra using the program DEX. This analysis determined that expression with a 10-fold excess of unlabeled amino acids relative to the 15N-amino acid prevents the scrambling of the 15N label that is observed when equimolar amounts are used. MALDI TOF-TOF MS/MS data provide additional information that shows where the “extra” 15N labels are incorporated, which can be useful in confirming ambiguous assignments. The described procedure provides a rapid technique to monitor the fidelity of selective labeling that does not require a lot of protein. These advantages make it an ideal way of determining optimal expression conditions for selectively labeled NMR samples. PMID:18567787

  13. Bioavailability of nitrogen from sewage sludge using 15N-labelled ammonium sulphate

    The high nutrient nitrogen and organic matter contents of sewage sludge (SS) make it a potential organic fertilizer for sandy soil. In this study, 15N-labelled ammonium sulphate was used to investigate the availability of nitrogen from irradiated and non-irradiated sewage sludge to tomato plants. The application of sewage sludge to sandy soil increased dry matter production (DMP), nitrogen yield (NY) and nitrogen recovery (NR) over two successive years. A positive relationship was found between sludge application rate and DMP and NY. The increase was significantly higher (P=0.05) in irradiated than non-irradiated sewage sludge. Total nitrogen derived from non-irradiated sewage sludge are : 48.0, 63.7, 73.5, 105.2 Kg/ha, whereas, the total nitrogen derived from irradiated sewage sludge are: 55.1, 72.5, 88.9, 141.4 Kg/ha corresponding to application rates of 10 t/ha, 20 t/ha, 30 t/ha, respectively. This was attributed to higher dry matter production in the later than the former. A highly significant correlation (0.945**) was found between dry matter production and sludge nitrogen yield (i.e. nitrogen derived from sewage sludge). Fertilizer nitrogen yield (total nitrogen derived from fertilizer) was high in treatment receiving mineral fertilizer, however, the 15N recovery by tomato was only 13.8%. Soil did not contribute well towards total nitrogen yield in tomato and most nitrogen was derived from sewage sludge. Percent nitrogen derived from sewage sludge was in the range 88-92%, depending on the application rate

  14. Nitrogen acquisition, transport and metabolism in intact ectomycorrhizal associations studied by 15N stable isotope techniques

    The focus of this thesis is on the external mycelium and its role in nitrogen uptake, assimilation and translocation. Tree seedlings in association with ectomycorrhizal fungi were grown in observation chambers. The fungal mycelium were fed with 15-N ammonium or 15-N nitrate or a combination of both. The effects of Collembola on the ectomycorrhizal symbiosis were also studied. The results demonstrates an important role of the external mycelium of Paxillus involutus not only in the uptake but also in the assimilation of ammonium into a variety of different amino acids, primarily glutamine but also glutamic acid, aspartic acid, and alanine, immediately after uptake. The results indicate that ammonium is assimilated by GS and GOGAT or GDH in the mycelium at the uptake site. When nitrate was added to the mycelium as the sole nitrogen source nitrate was reduced in the mycelium and the product assimilated into amino acids. When ammonium nitrate was supplied to the fungal mycelium nitrate was taken up the fungus and transferred to the plant, however, apparently no assimilation of nitrate occurred in the external mycelium. Ammonium or an assimilation product, such as glutamine, probably represses nitrate reductase (NR) but not nitrate uptake and transfer in P. involutus. P. involutus nitrogen uptake and transfer to the associated mycorrhizal pine was up to 76% higher when low numbers of the Collembola Onychiurus armatus were present compared to when they were completely absent. This was probably an indirect effect as P. involutus hyphal growth rate and extramatrical biomass increased at a low Collembola density. At high Collembola densities P. involutus hyphal growth rate was retarded. (74 refs.)

  15. Intraskeletal isotopic compositions (δ(13) C, δ(15) N) of bone collagen: nonpathological and pathological variation.

    Olsen, Karyn C; White, Christine D; Longstaffe, Fred J; von Heyking, Kristin; McGlynn, George; Grupe, Gisela; Rühli, Frank J

    2014-04-01

    Paleodiet research traditionally interprets differences in collagen isotopic compositions (δ(13) C, δ(15) N) as indicators of dietary distinction even though physiological processes likely play some role in creating variation. This research investigates the degree to which bone collagen δ(13) C and δ(15) N values normally vary within the skeleton and examines the influence of several diseases common to ancient populations on these isotopic compositions. The samples derive from two medieval German cemeteries and one Swiss reference collection and include examples of metabolic disease (rickets/osteomalacia), degenerative joint disease (osteoarthritis), trauma (fracture), infection (osteomyelitis), and inflammation (periostitis). A separate subset of visibly nonpathological skeletal elements from the German collections established normal intraindividual variation. For each disease type, tests compared bone lesion samples to those near and distant to the lesions sites. Results show that normal (nonpathological) skeletons exhibit limited intraskeletal variation in carbon- and nitrogen-isotope ratios, suggesting that sampling of distinct elements is appropriate for paleodiet studies. In contrast, individuals with osteomyelitis, healed fractures, and osteoarthritis exhibit significant intraskeletal differences in isotope values, depending on whether one is comparing lesions to near or to distant sites. Skeletons with periostitis result in significant intraskeletal differences in nitrogen isotope values only, while those with rickets/osteomalacia do not exhibit significant intraskeletal differences. Based on these results, we suggest that paleodiet researchers avoid sampling collagen at or close to lesion sites because the isotope values may be reflecting both altered metabolic processes and differences in diet relative to others in the population. PMID:24374993

  16. The Use of 32P and 15N to Estimate Fertilizer Efficiency in Oil Palm

    Oil palm has become an important commodity for Indonesia reaching an area of 2.6 million ha at the end of 1998. It is mostly cultivated in highly weathered acid soil usually Ultisols and Oxisols which are known for their low fertility, concerning the major nutrients like N and P. This study most conducted to search for the most active root-zone of oil palm and applied urea fertilizer at such soils to obtain high N-efficiency. Carrier free KH232PO4 solution was used to determine the active root-zone of oil palm by applying 32P around the plant in twenty holes. After the most active root-zone have been determined, urea in one, two and three splits were respectively applied at this zone. To estimate N-fertilizer efficiency of urea labelled 15N Ammonium Sulphate was used by adding them at the same amount of 16 g 15N plan-1. This study showed that the most active root-zone was found at a 1.5 m distance from the plant-stem and at 5 cm soil depth. For urea the highest N-efficiency was obtained from applying it at two splits. The use of 32P was able to distinguish several root zones: 1.5 m - 2.5 m from the plant-stem at a 5 cm and 15 cm soil depth. Urea placed at the most active root-zone, which was at a 1.5 m distance from the plant-stem and at a 5 cm depth in one, two, and three splits respectively showed difference N-efficiency. The highest N-efficiency of urea was obtained when applying it in two splits at the most active root-zone. (author)

  17. Evaluation of nitrogen sources in two barley varieties using the isotopic dilution method (15N)

    Two barley varieties (Leo and Granifen) were sown under field conditions in two different soils (Vilcun and Collipulli series) in the south of Chile, to evaluate each genotype behaviour after applying four nitrogenous fertilizers: Urea (U), Sodium Chilean Nitrate (SS), Ammonium Nitrate (AN), and Ammonium Sulfate (AS), at a rate of 70 kg N ha1 in the Vilcun serie and 90 kg N ha1 in the Collipulli serie. The 15N isotopic dilution method was used, labelling the soil with 20 kg N ha1 AS enriched with 10% at. exc. 15N as a standard fertilizer. The statistical design was that of completely randomized blocks with five treatments and four replicates. Plants were harvested when physiologically mature, dried, and ground into three fractions (leaves + stem, grains, and chaff) to measure the agronomic (dry matter yield and total N), and isotopic parameters (nitrogen derived from fertilizer, nitrogen derived from soil, fertilizer use efficiency, and A value). The grain Ndffu (kg ha1) was higher in Leo's variety than in Granifen, mainly using the SS fertilizer. The same behaviour showed the Fertilizer Use Efficiency (FUE, %) parameter. On the other hand, Granifen showed the greatest Nddfu (kg ha1) using SS in Collipulli's serie than in Vilcun. However, in Collipulli's serie, Granifen showed lowest percentage using AS as source. Regarding the nitrogen source equivalence, considering SS as a reference, it is observed that in Leo's variety it is possible to apply any fertilizer to reach the same result. For Granifen, serie Vilcun, with SS as a reference, it is necessary to have between 1,4 and 1,6 kg of the other sources in order to get the same result. For the same variety and the same fertilizer reference, in the serie Collipulli, 2,5 kg of AS are required to reach the same result

  18. Appraisal of {sup 15}N enrichment and {sup 15}N natural abundance methods for estimating N{sub 2} fixation by understorey Acacia leiocalyx and A. disparimma in a native forest of subtropical Australia

    Bai, Shahla Hosseini; Xu, Zhihong; Blumfield, Timothy J. [Griffith Univ., Nathan, Brisbane, QLD (Australia). School of Biomolecular and Physical Sciences, Environmental Futures Centre; Sun, Fangfang [Guangdong Academy of Agricultural Sciences, Guangzhou (China). Research Centre for Quality, Safety and Standard of Agricultural Products; Chen, Chengrong [Griffith Univ., Nathan, Brisbane, QLD (Australia). School of Environment, Environmental Futures Centre; Wild, Clyde [Griffith Univ., Gold Coast, QLD (Australia). School of Environment, Environmental Futures Centre

    2012-05-15

    Purpose: It is anticipated that global climate change will increase the frequency of wildfires in native forests of eastern Australia. Understorey legumes such as Acacia species play an important role in maintaining ecosystem nitrogen (N) balance through biological N fixation (BNF). This is particularly important in Australian native forests with soils of low nutrient status and frequent disturbance of the nutrient cycles by fires. This study aimed to examine {sup 15}N enrichment and {sup 15}N natural abundance techniques in terms of their utilisation for evaluation of N{sub 2} fixation of understorey acacias and determine the relationship between species ecophysiological traits and N{sub 2} fixation. Materials and methods: A trial was established at sites 1 and 2 located at Toohey Forest, Queensland, Australia, a eucalypt-dominated native forest, to examine the determination of BNF using {sup 15}N enrichment and {sup 15}N natural abundance methods. Toohey Forest is an urban forest and subjected to frequent fuel reduction burns to protect the adjacent properties. Plant physiological status was measured to determine the relationship between physiological and N{sub 2} fixation activities. Results and discussion: Both {sup 15}N enrichment and {sup 15}N natural abundance techniques may be used to estimate N{sub 2} fixation of acacia tree species. The estimation of BNF using {sup 15}N enrichment was higher than those of the {sup 15}N natural abundance method. A grass reference plant, Themeda triandra, as well as tree reference plants provided an appropriate {delta}{sup 15}N signal. Potential B values for Acacia spp. between -0.3 permille and 1.0 permille provided an acceptable BNF estimation. This suburban forest is located nearby a busy highway leading to N deposition over time with consequent negative {delta}{sup 15}N signal. This N deposition may explain the separation between the {delta}{sup 15}N signal of the acacias and that of the reference plants which led to

  19. Backbone (1)H, (13)C, and (15)N NMR assignment for the inactive form of the retroviral protease of the murine intracisternal A-type particle, inMIA-14 PR

    Motáčková, V.; Kubíčková, M.; Kožíšek, Milan; Grantz Šašková, Klára; Švec, Martin; Žídek, L.; Sklenář, V.

    2009-01-01

    Roč. 3, č. 2 (2009), s. 261-264. ISSN 1874-2718 R&D Projects: GA MŠk LC512 Grant ostatní: GA MŠk(CZ) LC06030 Institutional research plan: CEZ:AV0Z40550506 Keywords : retroviral protease * MIA-14 PR * DNA binding domain * homodimer * NMR Subject RIV: CE - Biochemistry Impact factor: 0.750, year: 2009

  20. Dynamics of the amino acid and protein metabolism of laying hens after the application of 15N-labelled wheat protein. 4

    12 colostomized laying hybrids with an 81% laying performance received 36 g wheat containing a 15N excess (15N') of 14.37 atom-% in a customary ration over 4 days. The wheat lysine contained 13.58 atom-% 15N', histidine 14.38 and arginine 13.63 atom-% 15N'. In the 4-day period of 15N' application 540 mg 15N', 18.1 mg lysine 15N', 21.5 mg histidine 15N' and 47.9 mg arginine 15N' were consumed per hen. Subsequently the animals received the same ration with unlabelled wheat. 12 h, 36 h, 60 h and 108 h after the last 15N' application 3 animals each were butchered. The atom-% 15N' of the lysine was below that of the two other basic and of the non-basic amino acids. The labelling of the amino acids of the egg white decreased rapidly 2 days after 15N' application. The atom-% of the 15N' of the yolk of egg, however, increased after the discontinuation and remained the same for 4 days after the last 15N' application. The 14N and 15N' amounts measured in the complete experiment period are distributed over the 3 basic and the 12 non-basic (excluding thioamino acids) amino acids in the white of egg for 14N as 25.0%:57.6% and for 15N' as 18.2%:57.5%. In the yolk of egg 28.5% 14N for the basic and 56.8% for the non-basic amino acids could be calculated; the corresponding values for 15N' were 17.8% and 55.5%. (author)

  1. Recuperação de 15N-ureia no sistema solo-planta de pastagem de capim-tanzânia Recovery of 15N-urea in soil-plant system of tanzania grass pasture

    Geraldo Bueno Martha Júnior

    2009-02-01

    Full Text Available O atrativo econômico e o impacto ambiental da adubação nitrogenada em pastagens dependem da eficiência de uso do nitrogênio (N do fertilizante no sistema solo-planta. Entretanto, a recuperação do 15N-ureia em pastagem de Panicum maximum cv. Tanzânia, uma das forrageiras mais utilizadas na intensificação de sistemas pastoris, permanece desconhecida. Este experimento, seguindo um delineamento de blocos completos casualizados, com quatro tratamentos (0, 40, 80 e 120 kg ha-1 de N-ureia e três repetições, foi realizado para determinar a recuperação do 15N-ureia pelo capim-tanzânia. A produção de forragem, o teor de N total e a quantidade de N na planta não foram afetados pelas doses de 15N-ureia, refletindo as elevadas perdas do N aplicado nas condições do experimento. Entretanto, a baixa eficiência agronômica do uso da ureia pode ser explicada pelo decréscimo da recuperação do N do fertilizante no sistema solo-planta com o aumento da dose de 15N-ureia em situações climáticas bastante adversas, que contribuíram para aumentar as perdas de 15N-ureia no sistema solo-planta.The economic attractiveness and negative environmental impact of nitrogen (N fertilization in pastures depend on the N use efficiency in the soil-plant system. However, the recovery of urea-15N by Panicum maximum cv. Tanzania pastures, one of the most widely used forage species in intensified pastoral systems, is still unknown. This experiment was conducted in a randomized complete block design with four treatments (0, 40, 80 and 120 kg ha-1 of N-urea and three replications, to determine the recovery of 15N urea by Tanzania grass. Forage production, total N content and N yield were not affected by fertilization (p > 0.05, reflecting the high losses of applied N under the experimental conditions. The recovery of 15N urea (% of applied N in forage and roots was not affected by fertilization levels (p > 0.05, but decreased exponentially in the soil and soil

  2. Biological Nitrogen Fixation and Microbial Biomass N in the Rhizosphere of Chickpea as Estimated by 15N Isotope Dilution Technique

    Pot experiment was carried out with chickpea that cultivated in virgin sandy soil and inoculated with Rhizobium (Rh), mycorrhizea (VAM) and mixture of both. The objective of this work is the estimation of biological nitrogen fixation (BNF) and microbial biomass N (MBN) contribution as affected by inoculation and N and P fertilizers levels under chickpea plants. Nitrogen gained from air (Ndf A) was determined using 15N isotope dilution technique, while the MBN was detected through the fumigation-extraction method. Nitrogen and phosphorus fertilizers were applied at three levels, 0; 10 ppm N and 3.3 ppm P and 20 ppm Nand 6.6 ppm P in the form of (15NH4)2SO4 and super-phosphate, respectively. The effect of inoculation and chemical fertilizers on dry matter (DM), N and P uptake (shoot and grain), BNF and MBN were traced. The obtained data revealed that the highest DM and N uptake by chickpea shoot were recorded with the dual inoculation (Rh + VAM) at the moderate level of N and P fertilizers, while the highest DM, N and P uptake by grain were recorded with Rh solely at the same rate of fertilizers. It was clear that inoculation with Rh either alone or in combination with VAM substituted considerable amounts of N via BNF process. In this respect, dual inoculation is still superior over single inoculation. Percentages of N2-fixed was ranged from 45% to 73% in shoot while it was 27% to 69% in grain according to inoculation and fertilization treatments. Fixed N utilized by shoot was positively affected by increasing the N fertilizer rate while that derived by grain was not affected. The fluctuation in the soil microbial biomass N did not gave us a chance to recognize, exactly, the impact of inoculation and/or fertilization levels. (Authors)

  3. O potencial da rotulação metabólica de 15N para a pesquisa de esquizofrenia The potential of 15N metabolic labeling for schizophrenia research

    Michaela D. Filiou

    2013-01-01

    Full Text Available Pesquisas em psiquiatria ainda necessitam de estudos não dirigidos por hipóteses para revelar fundamentos neurobiológicos e biomarcadores moleculares para distúrbios psiquiátricos. Metodologias proteômicas disponibilizam uma série de ferramentas para esses fins. Apresentamos o princípio de rotulação metabólica utilizando 15N para proteômica quantitativa e suas aplicações em modelos animais de fenótipos psiquiátricos com um foco particular em esquizofrenia. Exploramos o potencial de rotulação metabólica por 15N em diferentes tipos de experimentos, bem como suas considerações metodológicas.Psychiatric research is in need of non-hypothesis driven approaches to unravel the neurobiological underpinnings and identify molecular biomarkers for psychiatric disorders. Proteomics methodologies constitute a state-of-the-art toolbox for biomarker discovery in psychiatric research. Here we present the principle of in vivo 15N metabolic labeling for quantitative proteomics experiments and applications of this method in animal models of psychiatric phenotypes, with a particular focus on schizophrenia. Additionally we explore the potential of 15N metabolic labeling in different experimental set-ups as well as methodological considerations of 15N metabolic labeling-based quantification studies.

  4. Studies on the protein and amino acid metabolism of laying hens using 15N-labelled casein. 8

    Four colostomized Leghorn hens were fed, during 6 days, 15N-labelled casein as sole protein source. Two animals were slaughtered 48 hours, the other two 144 hours after the last 15N-application. The share of TCE-soluble N in total N averaged 16% for the body parts analysed, i.e. meat, bone, liver, kidneys, oviducts, residual viscera and other. The variation of the lysine, histidine and arginine levels in the body parts ranged from 3.6 to 7.9 g, 1.1 to 3.7 g and 6.4 to 7.4 g in 16.7 g hydrolysate N, respectively. Except for feathers, the analysed body parts contained an excess amount of heavy nitrogen. The degree of labelling was found to depend on the time of slaughtering after the tracer application. In the liver and in the oviduct being metabolically active organs, the 15N-excess in the total N fraction decreased by 45% between the 2nd and the 6th days after 15N-feeding, whilst in the meat it went down by 20%. The decline of the 15N-concentration in the TCE-soluble N compounds was faster than in the total N-fraction. Out of the body samples analysed, the lysine of the liver having 0.26 atom% 15N-excess was found to be more strongly labelled in hens 1 and 2. The amino acid arginine reached about the same level of labelling, the 15N-frequency of histidine being the lowest. (author)

  5. Nitrogen and water utilization by trickle fertigated garlic using the neutron gauge and 15N technologies

    The objective of this study was to increase water and fertilizer use efficiency for conventional fertilization and fertigation. The following treatments were included and studied in an RCB design with four replications of each treatment: Zero N, 30, 60 and 90 ppm N in the irrigation water. Additional soil application equivalent to one fertigation treatment was also included. The fertilizers were injected into the irrigation water by means of an injection pump. Garlic was planted in plot with dimensions of 3mx4.5m. Irrigation was applied to replenish 80% of the Class A pan evaporation on a weekly bases. Access tubes for neutron probe reading were mounted in each plot in three replications. The readings were taken before and after each irrigation or rainfall at 15, 30, 45, 60 and 90 cm soil depth. The labelled N fertilizers (15N) were applied to microplots which contained five plants within each plot. At harvest, plant samples were taken from the microplots for the 15N measurements. Plant samples were collected and prepared according to the instructions for sampling for 15N analysis. The yield and its components were obtained from the macroplot. The yield continued to increase with increasing N fertigation rates. The fresh weight per head and per segment showed a similar trend as the yield did. However, the number of segments per head was not affected significantly by the investigated treatments in this study. This may indicate that the zero N treatments produced heads with small segments compared to that produced with N application. The dry weight of shoot, segment and segment membrane responded positively to the rates of N fertigation, reaching the maximum value at the rates of 80 and 120 kg N, irrespective of N fertigation or soil application. The soil application gave a production as high as the best fertigated N rate but lower than the zero N treatment. The percentage of N content in fruits and leaves was the highest with the fertigation treatments where the

  6. Nature of organic carbon and nitrogen in physically protected organic matter of some Australian soils as revealed by solid-state 13 C and 15 N NMR spectroscopy

    The 13C and 15N nuclear magnetic resonance (NMR) spectroscopy was applied for characterising the chemical nature of the remaining organic fraction. The 13C NMR spectroscopic comparison of the residues after UV photo-oxidation and the untreated bulk soils revealed a considerable increase in condensed aromatic structures in the residues for 4 of the 5 soils. This behaviour was recently shown to be typical for char-containing soils. In the sample where no char was detectable by NMR spectroscopy, the physically protected carbon consisted of functional groups similar to those observed for the organic matter of the bulk sample, although their relative proportions were altered. The solid-state 15N NMR spectrum from this sample revealed that some peptide structures were able to resist UV photo-oxidation, probably physically protected within the core of micro aggregates. Heterocyclic aromatic nitrogen was not detected in this spectrum, but pyrrolic nitrogen was found to comprise a major fraction of the residues after photo-oxidation of the <53 μm containing soils. Acid hydrolysis of these samples confirmed that some peptide-like material was still present. The identification of a considerable amount of aromatic carbon and nitrogen, assignable to charred material in 4 of the 5 investigated soils, supports previous observations that char largely comprises the inert or passive organic matter pool of many Australian soils. The influence of such material on the carbon and nitrogen dynamics in such soils, however, requires further research. Copyright (2000) CSIRO Australia

  7. Fate of 15N fertilizer applied to trickle-irrigated grapevines

    Information on fate of nitrogen applied to vines is needed to improve fertilizer management. Nitrogen-15 enriched ammonium and nitrate fertilizers were applied in the spring through a trickle irrigation system to six Thompson Seedless vines of a vineyard on the West Side of the San Joaquin Valley of California. At fruit harvest, all above-ground plant parts were removed and analyzed for 15N. Soil around each vine was also sampled and analyzed for 15N in the inorganic and organic N fractions. Spatial patterns of fertilizer N for soil inorganic and organic N were analyzed using a median polish technique which indicated large variability with respect to direction, distance, and depth. There was a tendency for the fertilizer N from NH4 to be located directly beneath emitters than from the NO3. Nitrogen from the NH4 application penetrated to only the 150-cm depth, whereas some N from the NO3 application reached 210 to 240 cm. Most of the organic fertilizer N for both NO3 and NH4 applications was in the top 60 cm of soil where the vine roots were likely of greatest density. Overall recovery of fertilizer N was also quite variable, probably due to variability in soil physical properties and uneven surface application of water and fertilizer due to local surface ponding. Although not statistically significant, uptake of fertilizer N by above-ground plant components was slightly higher for the NH4 application (24.2% of applied N) than the NO3 application (21.5%). Soil organic N had significantly (95% level) higher N from NH4 (19% of applied N) than from NO3 (13%). This probably occurred due to longer residence time of N from NH4 within the top 60 cm, where the bulk of roots and microbial activity existed, than for NO3. Overall, about 67% to 79% of the fertilizer N applied in spring remained in the soil at harvest, and the vines took up the rest. There was no indication of significant N leaching below 2.4 m or denitrification of fertilizer N for the trickle-irrigated vines

  8. A New Secondary Structure Assignment Algorithm Using Cα Backbone Fragments.

    Cao, Chen; Wang, Guishen; Liu, An; Xu, Shutan; Wang, Lincong; Zou, Shuxue

    2016-01-01

    The assignment of secondary structure elements in proteins is a key step in the analysis of their structures and functions. We have developed an algorithm, SACF (secondary structure assignment based on Cα fragments), for secondary structure element (SSE) assignment based on the alignment of Cα backbone fragments with central poses derived by clustering known SSE fragments. The assignment algorithm consists of three steps: First, the outlier fragments on known SSEs are detected. Next, the remaining fragments are clustered to obtain the central fragments for each cluster. Finally, the central fragments are used as a template to make assignments. Following a large-scale comparison of 11 secondary structure assignment methods, SACF, KAKSI and PROSS are found to have similar agreement with DSSP, while PCASSO agrees with DSSP best. SACF and PCASSO show preference to reducing residues in N and C cap regions, whereas KAKSI, P-SEA and SEGNO tend to add residues to the terminals when DSSP assignment is taken as standard. Moreover, our algorithm is able to assign subtle helices (310-helix, π-helix and left-handed helix) and make uniform assignments, as well as to detect rare SSEs in β-sheets or long helices as outlier fragments from other programs. The structural uniformity should be useful for protein structure classification and prediction, while outlier fragments underlie the structure-function relationship. PMID:26978354

  9. Solid state radiation chemistry of the DNA backbone

    The long term goal of this program is to determine the fundamental rules needed to predict the type and yield of damage produced in DNA due to direct effects of ionizing radiation. The focus is on damage to the sugar-phosphate backbone, damage that would lead to strand breaks. Model systems have been chosen that permit various aspects of this problem to be investigated. The emphasis will be on single crystals of monosaccharides, nucleosides, and nucleotides but will also include some powder work on polynucleotides. In these model systems, free radical products and reactions are observed by electron spin resonance (ESR) and electron nuclear double resonance (ENDOR) techniques. The information thus gained is used in constructing rules that predict what primary free radicals are formed in single crystals of model compounds and the reactions stemming from the primary radicals. The formulation of a set of rules that work in model systems will represent a major advance toward formulating a set of rules that predict the direct damage in DNA itself. In a broader context this program is part of the effort to understand and predict the effects of exposure to ionizing radiation received at low dose rates over long periods of time. Assessment of low dose effects requires a basic understanding of the action of radiation at the molecular level. By contributing to that basic understanding, this program will help solve the problems of risk assessment under low dose conditions. 5 refs., 3 figs

  10. Backbone of complex networks of corporations: The flow of control

    Glattfelder, J. B.; Battiston, S.

    2009-09-01

    We present a methodology to extract the backbone of complex networks based on the weight and direction of links, as well as on nontopological properties of nodes. We show how the methodology can be applied in general to networks in which mass or energy is flowing along the links. In particular, the procedure enables us to address important questions in economics, namely, how control and wealth are structured and concentrated across national markets. We report on the first cross-country investigation of ownership networks, focusing on the stock markets of 48 countries around the world. On the one hand, our analysis confirms results expected on the basis of the literature on corporate control, namely, that in Anglo-Saxon countries control tends to be dispersed among numerous shareholders. On the other hand, it also reveals that in the same countries, control is found to be highly concentrated at the global level, namely, lying in the hands of very few important shareholders. Interestingly, the exact opposite is observed for European countries. These results have previously not been reported as they are not observable without the kind of network analysis developed here.

  11. Data acquisition backbone core DABC release v1.0

    The new experiments at FAIR require new concepts of data acquisition systems for the distribution of self-triggered, time stamped data streams over high performance networks for event building. The Data Acquisition Backbone Core (DABC) is a general purpose software framework developed for the implementation of such data acquisition systems. A DABC application consists of functional components like data input, combiner, scheduler, event builder, filter, analysis and storage which can be configured at runtime. Application specific code including the support of all kinds of data channels (front-end systems) is implemented by C++ program plug-ins. DABC is also well suited as environment for various detector and readout components test beds. A set of DABC plug-ins has been developed for the FAIR experiment CBM (Compressed Baryonic Matter) at GSI. This DABC application is used as DAQ system for test beamtimes. Front-end boards equipped with n-XYTER ASICs and ADCs are connected to read-out controller boards (ROC). From there the data is sent over Ethernet (UDP), or over optics and PCIe interface cards into Linux PCs. DABC does the controlling, event building, archiving and data serving. The first release of DABC was published in 2009 and is available under GPL license.

  12. Dynamics of the amino acid and protein metabolism of laying hens after the application of 15N-labelled wheat protein. 5

    12 colostomized laying hens which received 15N-labelled wheat over 4 days were butchered 12 h, 36 h, and 108 h (3 animals each) after the last 15N application. The intake of 15N exess (15N') from the wheat amounted to 540 mg 15N' during the application period. The 15N' in the blood plasma decreased after the last 15N' application from 0.76 atom-% to 0.55 atom-% after 108 h, the labelling of the corpuscular components at the same measuring points increased from 0.28 to 0.50 atom-% 15N'. 96.6% of the plasma 15N' and 93,8% of that in the corpuscles is precipitable in trichloroacetic acid. The atom-% 15N' of histidine in the total blood remained unchanged in dependence on the butchering time. The 15N amount in lysine and arginine and that in the non-basic amino acids decreased inconsiderably in the period between 12 h and 108 h after the last 15N' wheat feeding. (author)

  13. Spin and parity determinations of excited 15N based on polarized and unpolarized 12C(7Li, α)15N reaction data at E lab = 34 MeV

    From an experiment conducted at the Florida State University Accelerator Laboratory with a 34 MeV polarized 7Li beam bombarding a 12C target, we have obtained angular distributions and analyzing powers for states of 15N up to 20 MeV in excitation energy. This study not only offers the possibility to assign spin and parity to several states in 15N, but also serves to obtain nuclear potential parameters used in Distorted Wave Born (DWBA) and Coupled Channel Born (CCBA) Approximations to generate theoretical angular distributions and vector analyzing powers that give the best description of the experimental data. Under the assumption that the reaction mechanism is a three nucleon transfer, the determination of shell model nucleonic configurations and spectroscopic factors is possible for the 15N states studied

  14. Does {delta} {sup 15}N in river food webs reflect the intensity and origin of N loads from the watershed?

    Anderson, Caroline [Departement de Chimie-Biologie, Universite du Quebec a Trois-Rivieres, 3351 Boul. Des Forges, CP 500, Trois-Rivieres, QC, G9A 5H7 (Canada)]. E-mail: Caroline.Anderson@uqtr.ca; Cabana, Gilbert [Departement de Chimie-Biologie, Universite du Quebec a Trois-Rivieres, 3351 Boul. Des Forges, CP 500, Trois-Rivieres, QC, G9A 5H7 (Canada)

    2006-08-31

    Stable nitrogen isotope ratios ({delta} {sup 15}N) were measured in invertebrates and fish collected from 82 river sites located in the Saint-Lawrence Lowlands in Quebec, Canada, to examine the relationship between aquatic biota {delta} {sup 15}N and anthropogenic nitrogen (N) loads. Mean {delta} {sup 15}N values of all three trophic levels examined (primary consumers, predatory invertebrates and invertebrate-feeding fish) were highly correlated with total anthropogenic N loads on the watershed (kg N km{sup -2} year{sup -1}; r {sup 2} > 0.61, p < 0.0001) and with N loads originating from livestock manure (r {sup 2} > 0.62, p < 0.0001), synthetic fertilizers (r {sup 2} > 0.45, p < 0.0001), and human population (r {sup 2} > 0.29, p < 0.0001), respectively. Significant relationships were also observed between primary consumer {delta} {sup 15}N and N loads originating from each of the three livestock species examined (bovines, pigs and poultry; p < 0.0001). Furthermore, all three animal species contributed significantly and independently in elevating primary consumer {delta} {sup 15}N (multiple r {sup 2} = 0.67, p < 0.0001). Curvilinear regressions were observed at all levels of analysis, {delta} {sup 15}N values increasing slowly over a wide range of low levels of N loads, but increasing much faster as N loads grew larger. The three anthropogenic N sources examined were highly correlated with one another, preventing us from statistically isolating their respective effects on {delta} {sup 15}N. When these loads were expressed as a proportion of total N load, {delta} {sup 15}N of aquatic biota was still highly correlated with N from livestock and fertilizers, but not with N from human population. Overall, these results suggest that {delta} {sup 15}N values of aquatic consumers could be used as indicators of the intensity of anthropogenic N loading on watersheds, but not as tracers of the relative importance of individual N sources.

  15. Elucidating the trophodynamics of four coral reef fishes of the Solomon Islands using δ15N and δ13C

    Greenwood, N. D. W.; Sweeting, C. J.; Polunin, N. V. C.

    2010-09-01

    Size-related diet shifts are important characteristics of fish trophodynamics. Here, body size-related changes in muscle δ15N and δ13C of four coral reef fishes, Acanthurus nigrofuscus (herbivore), Chaetodon lunulatus (corallivore) , Chromis xanthura (planktivore) and Plectropomus leopardus (piscivore) were investigated at two locations in the Solomon Islands. All four species occupied distinct isotopic niches and the concurrent δ13C' values of C. xanthura and P. leopardus suggested a common planktonic production source. Size-related shifts in δ15N, and thus trophic level, were observed in C. xanthura, C. lunulatus and P. leopardus, and these trends varied between location, indicating spatial differences in trophic ecology. A literature review of tropical fishes revealed that positive δ15N-size trends are common while negative δ15N-size trends are rare. Size-δ15N trends fall into approximately equal groups representing size-based feeding within a food chain, and that associated with a basal resource shift and occurs in conjunction with changes in production source, indicated by δ13C. The review also revealed large scale differences in isotope-size trends and this, combined with small scale location differences noted earlier, highlights a high degree of plasticity in the reef fishes studied. This suggests that trophic size analysis of reef fishes would provide a productive avenue to identify species potentially vulnerable to reef impacts as a result of constrained trophic behaviour.

  16. Photosynthetic 14CO2 fixation and [15N]-ammonia assimilation during UV-B radiation of Lithodesmium variabile

    Uptake of [15N]-ammonia was more sensitive to UV-B exposure than the total 14CO2 fixation rate of Lithodesmium variabile Takano. Short-term UV-B radiation (15 min) had practically no effect on the kinetics of [15N]-ammonia, whereas there was an effect on [14C]-bicarbonate uptake rate. A significant reduction was found after 30 and 60 min UV-B stress. The time course of photosynthetic uptake of 15NH4Cl at several wavelengths was markedly depressed at shorter wavelengths (irradiation with WG 280). A short-term (11 min) exposure to ultraviolet radiation had no influence on the [14C]-labeled photosynthetic products. However, the [15N]-label of several amino acids and the ratio of [15N]-glutamine to [15N]-glutamic acid varied after irradiation with different ultraviolet wavebands. The results are discussed with reference to UV damage to the key enzymes of nitrogen metabolism. (author)

  17. Use of 15N enriched plant material for labelling of soil nitrogen in legume dinitrogen fixation experiments

    The soil nitrogen in a field plot was labelled with nitrogen-15 (15N) by incorporating labelled plant material derived from previous experiments. The plot was used the following 3 years for determination of the amount of N2 fixed by different leguminous plants. The atom % 15N excess in grains of cereals grown as reference crops was 0.20, 0.05 and 0.03 in the 3 years, respectively. In the first year the level of enrichment was adequate for estimating symbiotic nitrogen fixation. In the second and third year lack of precision in determination of the 15N/14N ratios of legume N, may have caused an error in estimates of nitrogen fixation. About 23% of the labelled N was taken up by plants during the 3 years of cropping; after 4 years about 44% of the labelled N was found still to be present in the top soil. The labelling of the soil nitrogen with organic bound 15N, compared to adding mineral 15N at sowing, is advantageous because the labelled N is released by mineralization so that the enrichment of the plant available soil N pool become more uniform during the growth season; and high levels of mineral N, which may depress the fixation process, is avoided. (author) 7 tabs., 1 ill., 30 refs

  18. Changes of free amino acids during rumen fermentation and incorporation of urea-15N into microorganisms in vitro

    Nitrogen-15 in urea was incorporated into NH3-N, bacteria-N, and 2,000 rpm-precipitate fraction-N with time course changes. The degree of incorporation was more intensely in U5 experiment than in U3 experiment. The highest 15N concentration in the bacterial fraction appeared after 6 and 12 hours after the beginning of incubation in the case of U3 and U5, respectively. The time course changes in 15N concentration in the 2,000 rpm-precipitate fraction were in parallel with that in the bacterial fraction except for 24 hours. The changes in concentration of free amino acids in the medium were observed in lysine, aspartic acid, and alanine remarkably. The concentration of total free amino acids changed with the lapse of time. The total concentration in the case of U3 experiment decreased gradually until 6 hours, and then increased until 24 hours. On the other hand, the total concentration in the case of U5 decreased continuously except for the slight increase at 6 hours. Each amino acid was isolated from the hydrolyzate of the 2,000 rpm-precipitate fraction by column chromatography. Each 15N concentration was determined for isolated amino acids. Consequently, 15N concentrations were relatively high in glysine, alanine, glutamic acid, and aspartic acid. On the contrary, 15N concentrations were very low in methionine and cystine. (JPN)

  19. Stellar Origins of Extremely $^{\\text{13}}C$- and $^{15}N$-enriched Presolar SiC Grains: Novae or Supernovae?

    Liu, Nan; Alexander, Conel M O'D; Wang, Jianhuan; Pignatari, Marco; Jose, Jordi; Nguyen, Ann

    2016-01-01

    Extreme excesses of $^{13}C$ ($^{12}C$/$^{13}C$<10) and $^{15}N$ ($^{14}N$/$^{15}N$<20) in rare presolar SiC grains have been considered diagnostic of an origin in classical novae, though an origin in core collapse supernovae (CCSNe) has also been proposed. We report C, N, and Si isotope data for 14 submicron- to micron-sized $^{13}C$- and $^{15}N$-enriched presolar SiC grains ($^{12}C$/$^{13}C$<16 and $^{14}N$/$^{15}N$<~100) from Murchison, and their correlated Mg-Al, S, and Ca-Ti isotope data when available. These grains are enriched in $^{13}C$ and $^{15}N$, but with quite diverse Si isotopic signatures. Four grains with $^{29,30}Si$ excesses similar to those of type C SiC grains likely came from CCSNe, which experienced explosive H burning occurred during explosions. The independent coexistence of proton- and neutron-capture isotopic signatures in these grains strongly supports heterogeneous H ingestion into the He shell in pre-supernovae. Two of the seven putative nova grains with $^{30}Si$ e...

  20. Evaluation of a 15 N plot design for estimating plant recovery of fertilizer nitrogen applied to sugar cane

    Two experiments were conducted on commercial sugar cene fields cropped with the variety SP70-1143, with the objective of evaluating a single row microplot design to determine plant recovery of 15 N fertilizer nitrogen. One of them used 15 N-aqua ammonia and 15 N-urea applied to two linear meter microplots of a ratoon crop (four replicates.) The second used one linear meter microplots (three replicates) which received 15 N-aqua ammonia only. The fertilizers were applied on 15cm deep furrows, located 25 cm from both sides of the cane row. One linear meter of ratoon cane, inside and outside of the microplot, and on the same and adjacent rows were harvested twelve months after fertilization. The results indicate the feasibility of using single row regments of ratoon cane with 15 N-fertilizer. The main advantages of this microplot design, when compared to the classical 3 contiguous row segments, is that only one third of the labeled fertilizer is needed. (author). 25 refs, 3 figs, 5 tabs