1H, 15N and 13C resonance assignments of the J-domain of co-chaperone Sis1 from Saccharomyces cerevisiae.

PubMed

Pinheiro, Glaucia M S; Amorim, Gisele C; Iqbal, Anwar; Ramos, C H I; Almeida, Fabio C L

2018-04-30

Protein folding in the cell is usually aided by molecular chaperones, from which the Hsp70 (Hsp = heat shock protein) family has many important roles, such as aiding nascent folding and participating in translocation. Hsp70 has ATPase activity which is stimulated by binding to the J-domain present in co-chaperones from the Hsp40 family. Hsp40s have many functions, as for instance the binding to partially folded proteins to be delivered to Hsp70. However, the presence of the J-domain characterizes Hsp40s or, by this reason, as J-proteins. The J-domain alone can stimulate Hsp70 ATPase activity. Apparently, it also maintains the same conformation as in the whole protein although structural information on full J-proteins is still missing. This work reports the 1 H, 15 N and 13 C resonance assignments of the J-domain of a Hsp40 from Saccharomyces cerevisiae, named Sis1. Secondary structure and order parameter prediction from chemical shifts are also reported. Altogether, the data show that Sis1 J-domain is highly structured and predominantly formed by α-helices, results that are in very good agreement with those previously reported for the crystallographic structure.

1H, 15N and 13C resonance assignments for free and IEEVD peptide-bound forms of the tetratricopeptide repeat domain from the human E3 ubiquitin ligase CHIP.

PubMed

Zhang, Huaqun; McGlone, Cameron; Mannion, Matthew M; Page, Richard C

2017-04-01

The ubiquitin ligase CHIP catalyzes covalent attachment of ubiquitin to unfolded proteins chaperoned by the heat shock proteins Hsp70/Hsc70 and Hsp90. CHIP interacts with Hsp70/Hsc70 and Hsp90 by binding of a C-terminal IEEVD motif found in Hsp70/Hsc70 and Hsp90 to the tetratricopeptide repeat (TPR) domain of CHIP. Although recruitment of heat shock proteins to CHIP via interaction with the CHIP-TPR domain is well established, alterations in structure and dynamics of CHIP upon binding are not well understood. In particular, the absence of a structure for CHIP-TPR in the free form presents a significant limitation upon studies seeking to rationally design inhibitors that may disrupt interactions between CHIP and heat shock proteins. Here we report the 1 H, 13 C, and 15 N backbone and side chain chemical shift assignments for CHIP-TPR in the free form, and backbone chemical shift assignments for CHIP-TPR in the IEEVD-bound form. The NMR resonance assignments will enable further studies examining the roles of dynamics and structure in regulating interactions between CHIP and the heat shock proteins Hsp70/Hsc70 and Hsp90.

Molecular beam electric resonance study of KCN, K 13CN and KC 15N

NASA Astrophysics Data System (ADS)

van Vaals, J. J.; Leo Meerts, W.; Dymanus, A.

1984-08-01

The microwave spectra of the isotopic species K 13CN and KC 15N have been investigated by molecular beam electric resonance spectroscopy, using the seeded beam technique. For both isotopic species about 20 rotational transitions originating in the ground vibrational state were observed in the frequency range 9-38 GHz. The observed transitions were fitted to an asymmetric rotor model to determine the three rotational, as well as the five quartic and three sextic centrifugal distortion constants. The hyperfine spectrum of KCN has been unravelled with the help of microwave-microwave double-resonance techniques. One hundred and forty hyperfine transitions in 11 rotational transitions have been assigned. The hyperfine structures of K 13CN and KC 15N were also studied. For all three isotopic species the quadrupole coupling constants and some spin-rotation coupling constants could be deduced. The rotational constants of the 13C and 15N isotopically substituted species of potassium cyanide, combined with those of the normal isotopic species (determined more accurately in this work), allowed an accurate and unambiguous evaluation of the structure, which was confirmed to be T shaped. Both the effective structure of the ground vibrational state and the substitution structure were evaluated. The results for the effective structural parameters are r CN = 1.169(3) Å, r KC = 2.716(9) Å, and r KN = 2.549(9) Å. The values obtained for the principal hyperfine coupling constant eQqz(N), the angle between the CN axis and zN, and the bond length rCN indicate that in gaseous potassium cyanide the CN group can be considered as an almost unperturbed CN - ion.

1H, 15N, 13C resonance assignment of folded and 8 M urea-denatured state of SUMO from Drosophila melanogaster.

PubMed

Kumar, Dinesh; Kumar, Ashutosh; Misra, Jyoti Ranjan; Chugh, Jeetender; Sharma, Shilpy; Hosur, Ramakrishna V

2008-06-01

SUMO, an important post-translational modifier of variety of substrate proteins, regulates different cellular functions. Here, we report the NMR resonance assignment of the folded and 8 M urea-denatured state of SUMO from Drosophila melanogaster (dsmt3).

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

PubMed Central

2012-01-01

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. PMID:22536902

NMR assignment of a PDZ domain in complex with a HPV51 E6 derived N-terminally pyroglutamic acid modified peptide.

PubMed

Mischo, André; Ohlenschläger, Oliver; Ramachandran, Ramadurai; Görlach, Matthias

2013-04-01

The resonance assignment of an amino-terminal pyroglutamic acid containing peptide derived from the E6 protein of human papillomavirus (HPV) type 51 in complex with PDZ domain 2 of hDlg/SAP-97 is reported. The assignments include (1)H, (13)C and (15)N resonances for the protein and peptide in the complex and all of the peptide's pyroglutamic acid nuclei.

Backbone resonance assignment of an insect arylalkylamine N-acetyltransferase from Bombyx mori reveals conformational heterogeneity.

PubMed

Aboalroub, Adam A; Zhang, Ziming; Keramisanou, Dimitra; Gelis, Ioannis

2017-04-01

Arylalkylamine N-acetyltransferases (AANATs) catalyze the transfer of an acetyl group from the acetyl-group donor, acetyl-CoA, to an arylalkylamine acceptor. Although a single AANAT has been identified in mammals, insects utilize multiple AANATs in a diverse array of biological processes. AANATs belong to the GCN5-related acetyltransferase (GNAT) superfamily of enzymes, which despite their overall very low sequence homology, are characterized by a well conserved catalytic core domain. The structural properties of many GNATs have been extensively studied by X-ray crystallography that revealed common features during the catalytic cycle. Here we report the 1 H, 13 C and 15 N backbone NMR resonance assignment of the 24 kDa AANAT3 from Bombyx mori (bmAANAT3) as a first step towards understanding the role of protein dynamics in the catalytic properties of AANATs. Our preliminary solution NMR studies reveal that bmAANAT3 is well-folded in solution. The P-loop, which is responsible for cofactor binding, is flexible in the free-state, while a large region of the enzyme interconverts between two distinct conformations in the slow exchange regime.

7 CFR 784.15 - Assignments.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 7 2010-01-01 2010-01-01 false Assignments. 784.15 Section 784.15 Agriculture Regulations of the Department of Agriculture (Continued) FARM SERVICE AGENCY, DEPARTMENT OF AGRICULTURE SPECIAL PROGRAMS 2004 EWE LAMB REPLACEMENT AND RETENTION PAYMENT PROGRAM § 784.15 Assignments. Any person...

NMR resonance assignments of the lantibiotic immunity protein NisI from Lactococcus lactis.

PubMed

Hacker, Carolin; Christ, Nina Alexandra; Duchardt-Ferner, Elke; Korn, Sophie; Berninger, Lucija; Kötter, Peter; Entian, Karl-Dieter; Wöhnert, Jens

2015-10-01

The lantibiotic nisin is a small antimicrobial peptide which acts against a wide range of Gram-positive bacteria. Nisin-producing Lactococcus lactis strains express four genes for self-protection against their own antimicrobial compound. This immunity system consists of the lipoprotein NisI and the ABC transporter NisFEG. NisI is attached to the outside of the cytoplasmic membrane via a covalently linked diacylglycerol anchor. Both the lipoprotein and the ABC transporter are needed for full immunity but the exact immunity mechanism is still unclear. To gain insights into the highly specific immunity mechanism of nisin producing strains on a structural level we present here the backbone resonance assignment of NisI (25.8 kDa) as well as the virtually complete (1)H,(15)N,(13)C chemical shift assignments for the isolated 12.7 kDa N-terminal and 14.6 kDa C-terminal domains of NisI.

Determination of γ -ray widths in 15N using nuclear resonance fluorescence

NASA Astrophysics Data System (ADS)

Szücs, T.; Bemmerer, D.; Caciolli, A.; Fülöp, Zs.; Massarczyk, R.; Michelagnoli, C.; Reinhardt, T. P.; Schwengner, R.; Takács, M. P.; Ur, C. A.; Wagner, A.; Wagner, L.

2015-07-01

Background: The stable nucleus 15N is the mirror of 15O, the bottleneck in the hydrogen burning CNO cycle. Most of the 15N level widths below the proton emission threshold are known from just one nuclear resonance fluorescence (NRF) measurement, with limited precision in some cases. A recent experiment with the AGATA demonstrator array determined level lifetimes using the Doppler shift attenuation method in 15O. As a reference and for testing the method, level lifetimes in 15N have also been determined in the same experiment. Purpose: The latest compilation of 15N level properties dates back to 1991. The limited precision in some cases in the compilation calls for a new measurement to enable a comparison to the AGATA demonstrator data. The widths of several 15N levels have been studied with the NRF method. Method: The solid nitrogen compounds enriched in 15N have been irradiated with bremsstrahlung. The γ rays following the deexcitation of the excited nuclear levels were detected with four high-purity germanium detectors. Results: Integrated photon-scattering cross sections of 10 levels below the proton emission threshold have been measured. Partial γ -ray widths of ground-state transitions were deduced and compared to the literature. The photon-scattering cross sections of two levels above the proton emission threshold, but still below other particle emission energies have also been measured, and proton resonance strengths and proton widths were deduced. Conclusions: Gamma and proton widths consistent with the literature values were obtained, but with greatly improved precision.

Bridge over troubled proline: assignment of intrinsically disordered proteins using (HCA)CON(CAN)H and (HCA)N(CA)CO(N)H experiments concomitantly with HNCO and i(HCA)CO(CA)NH.

PubMed

Hellman, Maarit; Piirainen, Henni; Jaakola, Veli-Pekka; Permi, Perttu

2014-01-01

NMR spectroscopy is by far the most versatile and information rich technique to study intrinsically disordered proteins (IDPs). While NMR is able to offer residue level information on structure and dynamics, assignment of chemical shift resonances in IDPs is not a straightforward process. Consequently, numerous pulse sequences and assignment protocols have been developed during past several years, targeted especially for the assignment of IDPs, including experiments that employ H(N), H(α) or (13)C detection combined with two to six indirectly detected dimensions. Here we propose two new HN-detection based pulse sequences, (HCA)CON(CAN)H and (HCA)N(CA)CO(N)H, that provide correlations with (1)H(N)(i - 1), (13)C'(i - 1) and (15)N(i), and (1)H(N)(i + 1), (13)C'(i) and (15)N(i) frequencies, respectively. Most importantly, they offer sequential links across the proline bridges and enable filling the single proline gaps during the assignment. We show that the novel experiments can efficiently complement the information available from existing HNCO and intraresidual i(HCA)CO(CA)NH pulse sequences and their concomitant usage enabled >95 % assignment of backbone resonances in cytoplasmic tail of adenosine receptor A2A in comparison to 73 % complete assignment using the HNCO/i(HCA)CO(CA)NH data alone.

Empirical Equation Based Chirality (n, m) Assignment of Semiconducting Single Wall Carbon Nanotubes from Resonant Raman Scattering Data

PubMed Central

Arefin, Md Shamsul

2012-01-01

This work presents a technique for the chirality (n, m) assignment of semiconducting single wall carbon nanotubes by solving a set of empirical equations of the tight binding model parameters. The empirical equations of the nearest neighbor hopping parameters, relating the term (2n− m) with the first and second optical transition energies of the semiconducting single wall carbon nanotubes, are also proposed. They provide almost the same level of accuracy for lower and higher diameter nanotubes. An algorithm is presented to determine the chiral index (n, m) of any unknown semiconducting tube by solving these empirical equations using values of radial breathing mode frequency and the first or second optical transition energy from resonant Raman spectroscopy. In this paper, the chirality of 55 semiconducting nanotubes is assigned using the first and second optical transition energies. Unlike the existing methods of chirality assignment, this technique does not require graphical comparison or pattern recognition between existing experimental and theoretical Kataura plot. PMID:28348319

A new algorithm for reliable and general NMR resonance assignment.

PubMed

Schmidt, Elena; Güntert, Peter

2012-08-01

The new FLYA automated resonance assignment algorithm determines NMR chemical shift assignments on the basis of peak lists from any combination of multidimensional through-bond or through-space NMR experiments for proteins. Backbone and side-chain assignments can be determined. All experimental data are used simultaneously, thereby exploiting optimally the redundancy present in the input peak lists and circumventing potential pitfalls of assignment strategies in which results obtained in a given step remain fixed input data for subsequent steps. Instead of prescribing a specific assignment strategy, the FLYA resonance assignment algorithm requires only experimental peak lists and the primary structure of the protein, from which the peaks expected in a given spectrum can be generated by applying a set of rules, defined in a straightforward way by specifying through-bond or through-space magnetization transfer pathways. The algorithm determines the resonance assignment by finding an optimal mapping between the set of expected peaks that are assigned by definition but have unknown positions and the set of measured peaks in the input peak lists that are initially unassigned but have a known position in the spectrum. Using peak lists obtained by purely automated peak picking from the experimental spectra of three proteins, FLYA assigned correctly 96-99% of the backbone and 90-91% of all resonances that could be assigned manually. Systematic studies quantified the impact of various factors on the assignment accuracy, namely the extent of missing real peaks and the amount of additional artifact peaks in the input peak lists, as well as the accuracy of the peak positions. Comparing the resonance assignments from FLYA with those obtained from two other existing algorithms showed that using identical experimental input data these other algorithms yielded significantly (40-142%) more erroneous assignments than FLYA. The FLYA resonance assignment algorithm thus has the

Backbone chemical shift assignments for the sensor domain of the Burkholderia pseudomallei histidine kinase RisS: "missing" resonances at the dimer interface.

PubMed

Buchko, Garry W; Edwards, Thomas E; Hewitt, Stephen N; Phan, Isabelle Q H; Van Voorhis, Wesley C; Miller, Samuel I; Myler, Peter J

2015-10-01

Using a deuterated sample, all the observable backbone (1)H(N), (15)N, (13)C(a), and (13)C' chemical shifts for the dimeric, periplasmic sensor domain of the Burkholderia pseudomallei histidine kinase RisS were assigned. Approximately one-fifth of the amide resonances are "missing" in the (1)H-(15)N HSQC spectrum and map primarily onto α-helices at the dimer interface observed in a crystal structure suggesting this region either undergoes intermediate timescale motion (μs-ms) and/or is heterogeneous.

A Markov Random Field Framework for Protein Side-Chain Resonance Assignment

NASA Astrophysics Data System (ADS)

Zeng, Jianyang; Zhou, Pei; Donald, Bruce Randall

Nuclear magnetic resonance (NMR) spectroscopy plays a critical role in structural genomics, and serves as a primary tool for determining protein structures, dynamics and interactions in physiologically-relevant solution conditions. The current speed of protein structure determination via NMR is limited by the lengthy time required in resonance assignment, which maps spectral peaks to specific atoms and residues in the primary sequence. Although numerous algorithms have been developed to address the backbone resonance assignment problem [68,2,10,37,14,64,1,31,60], little work has been done to automate side-chain resonance assignment [43, 48, 5]. Most previous attempts in assigning side-chain resonances depend on a set of NMR experiments that record through-bond interactions with side-chain protons for each residue. Unfortunately, these NMR experiments have low sensitivity and limited performance on large proteins, which makes it difficult to obtain enough side-chain resonance assignments. On the other hand, it is essential to obtain almost all of the side-chain resonance assignments as a prerequisite for high-resolution structure determination. To overcome this deficiency, we present a novel side-chain resonance assignment algorithm based on alternative NMR experiments measuring through-space interactions between protons in the protein, which also provide crucial distance restraints and are normally required in high-resolution structure determination. We cast the side-chain resonance assignment problem into a Markov Random Field (MRF) framework, and extend and apply combinatorial protein design algorithms to compute the optimal solution that best interprets the NMR data. Our MRF framework captures the contact map information of the protein derived from NMR spectra, and exploits the structural information available from the backbone conformations determined by orientational restraints and a set of discretized side-chain conformations (i.e., rotamers). A Hausdorff

1H, 15N, 13C resonance assignment of human GAP-43.

PubMed

Flamm, Andrea Gabriele; Żerko, Szymon; Zawadzka-Kazimierczuk, Anna; Koźmiński, Wiktor; Konrat, Robert; Coudevylle, Nicolas

2016-04-01

GAP-43 is a 25 kDa neuronal intrinsically disordered protein, highly abundant in the neuronal growth cone during development and regeneration. The exact molecular function(s) of GAP-43 remains unclear but it appears to be involved in growth cone guidance and actin cytoskeleton organization. Therefore, GAP-43 seems to play an important role in neurotransmitter vesicle fusion and recycling, long-term potentiation, spatial memory formation and learning. Here we report the nearly complete assignment of recombinant human GAP-43.

Contact replacement for NMR resonance assignment.

PubMed

Xiong, Fei; Pandurangan, Gopal; Bailey-Kellogg, Chris

2008-07-01

Complementing its traditional role in structural studies of proteins, nuclear magnetic resonance (NMR) spectroscopy is playing an increasingly important role in functional studies. NMR dynamics experiments characterize motions involved in target recognition, ligand binding, etc., while NMR chemical shift perturbation experiments identify and localize protein-protein and protein-ligand interactions. The key bottleneck in these studies is to determine the backbone resonance assignment, which allows spectral peaks to be mapped to specific atoms. This article develops a novel approach to address that bottleneck, exploiting an available X-ray structure or homology model to assign the entire backbone from a set of relatively fast and cheap NMR experiments. We formulate contact replacement for resonance assignment as the problem of computing correspondences between a contact graph representing the structure and an NMR graph representing the data; the NMR graph is a significantly corrupted, ambiguous version of the contact graph. We first show that by combining connectivity and amino acid type information, and exploiting the random structure of the noise, one can provably determine unique correspondences in polynomial time with high probability, even in the presence of significant noise (a constant number of noisy edges per vertex). We then detail an efficient randomized algorithm and show that, over a variety of experimental and synthetic datasets, it is robust to typical levels of structural variation (1-2 AA), noise (250-600%) and missings (10-40%). Our algorithm achieves very good overall assignment accuracy, above 80% in alpha-helices, 70% in beta-sheets and 60% in loop regions. Our contact replacement algorithm is implemented in platform-independent Python code. The software can be freely obtained for academic use by request from the authors.

Use of 15N reverse gradient two-dimensional nuclear magnetic resonance spectroscopy to follow metabolic activity in Nicotiana plumbaginifolia cell-suspension cultures.

PubMed

Mesnard, F; Azaroual, N; Marty, D; Fliniaux, M A; Robins, R J; Vermeersch, G; Monti, J P

2000-02-01

Nitrogen metabolism was monitored in suspension cultured cells of Nicotiana plumbaginifolia Viv. using nuclear magnetic resonance (NMR) spectroscopy following the feeding of (15NH4)2SO4 and K15NO3. By using two-dimensional 15N-1H NMR with heteronuclear single-quantum-coherence spectroscopy and heteronuclear multiple-bond-coherence spectroscopy sequences, an enhanced resolution of the incorporation of 15N label into a range of compounds could be detected. Thus, in addition to the amino acids normally observed in one-dimensional 15N NMR (glutamine, aspartate, alanine), several other amino acids could be resolved, notably serine, glycine and proline. Furthermore, it was found that the peak normally assigned to the non-protein amino-acid gamma-aminobutyric acid in the one-dimensional 15N NMR spectrum was resolved into a several components. A peak of N-acetylated compounds was resolved, probably composed of the intermediates in arginine biosynthesis, N-acetylglutamate and N-acetylornithine and, possibly, the intermediate of putrescine degradation into gamma-aminobutyric acid, N-acetylputrescine. The occurrence of 15N-label in agmatine and the low detection of labelled putrescine indicate that crucial intermediates of the pathway from glutamate to polyamines and/or the tobacco alkaloids could be monitored. For the first time, labelling of the peptide glutathione and of the nucleotide uridine could be seen.

Automated and assisted RNA resonance assignment using NMR chemical shift statistics

PubMed Central

Aeschbacher, Thomas; Schmidt, Elena; Blatter, Markus; Maris, Christophe; Duss, Olivier; Allain, Frédéric H.-T.; Güntert, Peter; Schubert, Mario

2013-01-01

The three-dimensional structure determination of RNAs by NMR spectroscopy relies on chemical shift assignment, which still constitutes a bottleneck. In order to develop more efficient assignment strategies, we analysed relationships between sequence and 1H and 13C chemical shifts. Statistics of resonances from regularly Watson–Crick base-paired RNA revealed highly characteristic chemical shift clusters. We developed two approaches using these statistics for chemical shift assignment of double-stranded RNA (dsRNA): a manual approach that yields starting points for resonance assignment and simplifies decision trees and an automated approach based on the recently introduced automated resonance assignment algorithm FLYA. Both strategies require only unlabeled RNAs and three 2D spectra for assigning the H2/C2, H5/C5, H6/C6, H8/C8 and H1′/C1′ chemical shifts. The manual approach proved to be efficient and robust when applied to the experimental data of RNAs with a size between 20 nt and 42 nt. The more advanced automated assignment approach was successfully applied to four stem-loop RNAs and a 42 nt siRNA, assigning 92–100% of the resonances from dsRNA regions correctly. This is the first automated approach for chemical shift assignment of non-exchangeable protons of RNA and their corresponding 13C resonances, which provides an important step toward automated structure determination of RNAs. PMID:23921634

Multiple-step relayed correlation spectroscopy: sequential resonance assignments in oligosaccharides.

PubMed Central

Homans, S W; Dwek, R A; Fernandes, D L; Rademacher, T W

1984-01-01

A general property of the high-resolution proton NMR spectra of oligosaccharides is the appearance of low-field well-resolved resonances corresponding to the anomeric (H1) and H2 protons. The remaining skeletal protons resonate in the region 3-4 ppm, giving rise to an envelope of poorly resolved resonances. Assignments can be made from the H1 and H2 protons to their J-coupled neighbors (H2 and H3) within this main envelope by using 1H-1H correlated spectroscopy. However, the tight coupling (J congruent to delta) between further protons results in poor spectral dispersion with consequent assignment ambiguities. We describe here three-step two-dimensional relayed correlation spectroscopy and show how it can be used to correlate the resolved anomeric (H1) and H2 protons with remote (H4, H5) protons directly through a linear network of couplings using sequential magnetization transfer around the oligosaccharide rings. Resonance assignments are then obtained by inspection of cross-peaks that appear in well-resolved regions of the two-dimensional spectrum. This offers a general solution to the assignment problem in oligosaccharides and, importantly, these assignments will subsequently allow for the three-dimensional solution conformation to be determined by using one-dimensional and two-dimensional nuclear Overhauser experiments. PMID:6593701

NMR assignments of the N-terminal domain of Nephila clavipes spidroin 1

PubMed Central

Parnham, Stuart; Gaines, William A.; Duggan, Brendan M.; Marcotte, William R.

2011-01-01

The building blocks of spider dragline silk are two fibrous proteins secreted from the major ampullate gland named spidroins 1 and 2 (MaSp1, MaSp2). These proteins consist of a large central domain composed of approximately 100 tandem copies of a 35–40 amino acid repeat sequence. Non-repetitive N and C-terminal domains, of which the C-terminal domain has been implicated to transition from soluble and insoluble states during spinning, flank the repetitive core. The N-terminal domain until recently has been largely unknown due to difficulties in cloning and expression. Here, we report nearly complete assignment for all 1H, 13C, and 15N resonances in the 14 kDa N-terminal domain of major ampullate spidroin 1 (MaSp1-N) of the golden orb-web spider Nephila clavipes. PMID:21152998

NMR resonance assignments of a hypoallergenic isoform of the major birch pollen allergen Bet v 1.

PubMed

Ahammer, Linda; Grutsch, Sarina; Wallner, Michael; Ferreira, Fatima; Tollinger, Martin

2017-10-01

In Northern America and Europe a great number of people are suffering from birch pollen allergy and pollen related food allergies. The trigger for these immunological reactions is the 17.5 kDa major birch pollen allergen Bet v 1, which belongs to the family of PR-10 (pathogenesis-related) proteins. In nature, Bet v 1 occurs as a mixture of various isoforms that possess different immunological properties despite their high sequence identities. Bet v 1.0102 (Bet v 1d), which is investigated here, is a hypoallergenic isoform of Bet v 1 and a potential candidate for allergen-specific immunotherapy. We assigned the backbone and side chain 1 H, 13 C and 15 N resonances of this protein and predicted its secondary structure. The NMR-chemical shift data indicate that Bet v 1.0102 is composed of three α-helices and a seven stranded β-sheet, in agreement with the known structure of the hyperallergenic isoform Bet v 1.0101 (Bet v 1a). Our resonance assignments create the foundation for detailed characterization of the dynamic properties of Bet v 1 isoforms by NMR relaxation measurements.

Reliable resonance assignments of selected residues of proteins with known structure based on empirical NMR chemical shift prediction

NASA Astrophysics Data System (ADS)

Li, Da-Wei; Meng, Dan; Brüschweiler, Rafael

2015-05-01

A robust NMR resonance assignment method is introduced for proteins whose 3D structure has previously been determined by X-ray crystallography. The goal of the method is to obtain a subset of correct assignments from a parsimonious set of 3D NMR experiments of 15N, 13C labeled proteins. Chemical shifts of sequential residue pairs are predicted from static protein structures using PPM_One, which are then compared with the corresponding experimental shifts. Globally optimized weighted matching identifies the assignments that are robust with respect to small changes in NMR cross-peak positions. The method, termed PASSPORT, is demonstrated for 4 proteins with 100-250 amino acids using 3D NHCA and a 3D CBCA(CO)NH experiments as input producing correct assignments with high reliability for 22% of the residues. The method, which works best for Gly, Ala, Ser, and Thr residues, provides assignments that serve as anchor points for additional assignments by both manual and semi-automated methods or they can be directly used for further studies, e.g. on ligand binding, protein dynamics, or post-translational modification, such as phosphorylation.

Reliable Resonance Assignments of Selected Residues of Proteins with Known Structure Based on Empirical NMR Chemical Shift Prediction

PubMed Central

Li, Da-Wei; Meng, Dan; Brüschweiler, Rafael

2015-01-01

A robust NMR resonance assignment method is introduced for proteins whose 3D structure has previously been determined by X-ray crystallography. The goal of the method is to obtain a subset of correct assignments from a parsimonious set of 3D NMR experiments of 15N, 13C labeled proteins. Chemical shifts of sequential residue pairs are predicted from static protein structures using PPM_One, which are then compared with the corresponding experimental shifts. Globally optimized weighted matching identifies the assignments that are robust with respect to small changes in NMR cross-peak positions. The method, termed PASSPORT, is demonstrated for 4 proteins with 100 – 250 amino acids using 3D NHCA and a 3D CBCA(CO)NH experiments as input producing correct assignments with high reliability for 22% of the residues. The method, which works best for Gly, Ala, Ser, and Thr residues, provides assignments that serve as anchor points for additional assignments by both manual and semi-automated methods or they can be directly used for further studies, e.g. on ligand binding, protein dynamics, or post-translational modification, such as phosphorylation. PMID:25863893

iHADAMAC: A complementary tool for sequential resonance assignment of globular and highly disordered proteins

NASA Astrophysics Data System (ADS)

Feuerstein, Sophie; Plevin, Michael J.; Willbold, Dieter; Brutscher, Bernhard

2012-01-01

An experiment, iHADAMAC, is presented that yields information on the amino-acid type of individual residues in a protein by editing the 1H- 15N correlations into seven different 2D spectra, each corresponding to a different class of amino-acid types. Amino-acid type discrimination is realized via a Hadamard encoding scheme based on four different spin manipulations as recently introduced in the context of the sequential HADAMAC experiment. Both sequential and intra-residue HADAMAC experiments yield highly complementary information that greatly facilitate resonance assignment of proteins with high frequency degeneracy, as demonstrated here for a 188-residue intrinsically disordered protein fragment of the hepatitis C virus protein NS5A.

Measurement of 1323 and 1487 keV resonances in 15N(α ,γ )19F with the recoil separator ERNA

NASA Astrophysics Data System (ADS)

Di Leva, A.; Imbriani, G.; Buompane, R.; Gialanella, L.; Best, A.; Cristallo, S.; De Cesare, M.; D'Onofrio, A.; Duarte, J. G.; Gasques, L. R.; Morales-Gallegos, L.; Pezzella, A.; Porzio, G.; Rapagnani, D.; Roca, V.; Romoli, M.; Schürmann, D.; Straniero, O.; Terrasi, F.; ERNA Collaboration

2017-04-01

Background: The origin of fluorine is a widely debated issue. Nevertheless, the 15N(α ,γ )19F reaction is a common feature among the various production channels so far proposed. Its reaction rate at relevant temperatures is determined by a number of narrow resonances together with the direct capture and the tails of the two broad resonances at Ec .m .=1323 and 1487 keV. Purpose: The broad resonances widths, Γγ and Γα, have to be measured with adequate precision in order to better determine their contribution to the 15N(α ,γ )19F stellar reaction rate. Methods: Measurement through the direct detection of the 19F recoil ions with the European Recoil separator for Nuclear Astrophysics (ERNA) were performed. The reaction was initiated by a 15N beam impinging onto a 4He windowless gas target. The observed yield of the resonances at Ec .m .=1323 and 1487 keV is used to determine their widths in the α and γ channels. Results: We show that a direct measurement of the cross section of the 15N(α ,γ )19F reaction can be successfully obtained with the recoil separator ERNA, and the widths Γγ and Γα of the two broad resonances have been determined. While a fair agreement is found with earlier determination of the widths of the 1487 keV resonance, a significant difference is found for the 1323 keV resonance Γα. Conclusions: The revision of the widths of the two more relevant broad resonances in the 15N(α ,γ )19F reaction presented in this work is the first step toward a more firm determination of the reaction rate. At present, the residual uncertainty at the temperatures of the 19F stellar nucleosynthesis is dominated by the uncertainties affecting the direct capture component and the 364 keV narrow resonance, both so far investigated only through indirect experiments.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Holliday, Michael; Zhang, Fengli; Isern, Nancy G.

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 isomerizationmore » 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.« less

7 CFR 636.15 - Offsets and assignments.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 7 Agriculture 6 2014-01-01 2014-01-01 false Offsets and assignments. 636.15 Section 636.15 Agriculture Regulations of the Department of Agriculture (Continued) NATURAL RESOURCES CONSERVATION SERVICE, DEPARTMENT OF AGRICULTURE LONG TERM CONTRACTING WILDLIFE HABITAT INCENTIVE PROGRAM § 636.15 Offsets and...

7 CFR 636.15 - Offsets and assignments.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 7 Agriculture 6 2012-01-01 2012-01-01 false Offsets and assignments. 636.15 Section 636.15 Agriculture Regulations of the Department of Agriculture (Continued) NATURAL RESOURCES CONSERVATION SERVICE, DEPARTMENT OF AGRICULTURE LONG TERM CONTRACTING WILDLIFE HABITAT INCENTIVE PROGRAM § 636.15 Offsets and...

7 CFR 636.15 - Offsets and assignments.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 6 2011-01-01 2011-01-01 false Offsets and assignments. 636.15 Section 636.15 Agriculture Regulations of the Department of Agriculture (Continued) NATURAL RESOURCES CONSERVATION SERVICE, DEPARTMENT OF AGRICULTURE LONG TERM CONTRACTING WILDLIFE HABITAT INCENTIVE PROGRAM § 636.15 Offsets and...

7 CFR 636.15 - Offsets and assignments.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 6 2013-01-01 2013-01-01 false Offsets and assignments. 636.15 Section 636.15 Agriculture Regulations of the Department of Agriculture (Continued) NATURAL RESOURCES CONSERVATION SERVICE, DEPARTMENT OF AGRICULTURE LONG TERM CONTRACTING WILDLIFE HABITAT INCENTIVE PROGRAM § 636.15 Offsets and...

7 CFR 636.15 - Offsets and assignments.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 6 2010-01-01 2010-01-01 false Offsets and assignments. 636.15 Section 636.15 Agriculture Regulations of the Department of Agriculture (Continued) NATURAL RESOURCES CONSERVATION SERVICE, DEPARTMENT OF AGRICULTURE LONG TERM CONTRACTING WILDLIFE HABITAT INCENTIVES PROGRAM § 636.15 Offsets and...

Mixed pyruvate labeling enables backbone resonance assignment of large proteins using a single experiment.

PubMed

Robson, Scott A; Takeuchi, Koh; Boeszoermenyi, Andras; Coote, Paul W; Dubey, Abhinav; Hyberts, Sven; Wagner, Gerhard; Arthanari, Haribabu

2018-01-24

Backbone resonance assignment is a critical first step in the investigation of proteins by NMR. This is traditionally achieved with a standard set of experiments, most of which are not optimal for large proteins. Of these, HNCA is the most sensitive experiment that provides sequential correlations. However, this experiment suffers from chemical shift degeneracy problems during the assignment procedure. We present a strategy that increases the effective resolution of HNCA and enables near-complete resonance assignment using this single HNCA experiment. We utilize a combination of 2- 13 C and 3- 13 C pyruvate as the carbon source for isotope labeling, which suppresses the one bond ( 1 J αβ ) coupling providing enhanced resolution for the Cα resonance and amino acid-specific peak shapes that arise from the residual coupling. Using this approach, we can obtain near-complete (>85%) backbone resonance assignment of a 42 kDa protein using a single HNCA experiment.

An automated framework for NMR resonance assignment through simultaneous slice picking and spin system forming.

PubMed

Abbas, Ahmed; Guo, Xianrong; Jing, Bing-Yi; Gao, Xin

2014-06-01

Despite significant advances in automated nuclear magnetic resonance-based protein structure determination, the high numbers of false positives and false negatives among the peaks selected by fully automated methods remain a problem. These false positives and negatives impair the performance of resonance assignment methods. One of the main reasons for this problem is that the computational research community often considers peak picking and resonance assignment to be two separate problems, whereas spectroscopists use expert knowledge to pick peaks and assign their resonances at the same time. We propose a novel framework that simultaneously conducts slice picking and spin system forming, an essential step in resonance assignment. Our framework then employs a genetic algorithm, directed by both connectivity information and amino acid typing information from the spin systems, to assign the spin systems to residues. The inputs to our framework can be as few as two commonly used spectra, i.e., CBCA(CO)NH and HNCACB. Different from the existing peak picking and resonance assignment methods that treat peaks as the units, our method is based on 'slices', which are one-dimensional vectors in three-dimensional spectra that correspond to certain ([Formula: see text]) values. Experimental results on both benchmark simulated data sets and four real protein data sets demonstrate that our method significantly outperforms the state-of-the-art methods while using a less number of spectra than those methods. Our method is freely available at http://sfb.kaust.edu.sa/Pages/Software.aspx.

Structure of 10 N in 9 C+p resonance scattering

DOE PAGES

Hooker, J.; Rogachev, G. V.; Goldberg, V. Z.; ...

2017-03-17

We studied the structure of exotic nucleus 10N using 9C+p resonance scattering. Two ℓ=0 resonances were found to be the lowest states in 10N. Furthermore, the ground state of 10N is unbound with respect to proton decay by 2.2(2) or 1.9(2) MeV depending on the 2 -or 1 -spin-parity assignment, and the first excited state is unbound by 2.8(2) MeV.

Vibrational spectra for uric acid and its D- and 15N-substituted analogues. Assignments for its normal modes from ab initio 3-21G force field.

NASA Astrophysics Data System (ADS)

Majoube, M.; Vergoten, G.

1993-03-01

FTR, Raman, FTIR spectra are obtained for polycrystalline uric acid and seven of its D-and 15N-substituted analogues. Assignments are given from a normal coordinate analysis carried out using a 3-21G ab initio force field. These are discussed by considering observed and calculated frequencies and D- and 15N-isotopic shifts.

1H, 13C and 15N resonance assignments and second structure information of Fag s 1: Fagales allergen from Fagus sylvatica

PubMed Central

Moraes, A. H.; Asam, C.; Batista, A.; Almeida, F. C. L.; Wallner, M.; Ferreira, F.; Valente, A. P.

2017-01-01

Fagales allergens belonging to the Bet v 1 family account responsible for the majority of spring pollinosis in the temperate climate zones in the Northern hemisphere. Among them, Fag s 1 from beech pollen is an important trigger of Fagales pollen associated allergic reactions. The protein shares high similarity with birch pollen Bet v 1, the best-characterized member of this allergen family. Of note, recent work on Bet v 1 and its homologues found in Fagales pollen demonstrated that not all allergenic members of this family have the capacity to induce allergic sensitization. Fag s 1 was shown to bind pre-existing IgE antibodies most likely primarily directed against other members of this multi-allergen family. Therefore, it is especially interesting to compare the structures of Bet v 1-like pollen allergens, which have the potential to induce allergic sensitization with allergens that are mainly cross-reactive. This in the end will help to identify allergy eliciting molecular pattern on Bet v 1-like allergens. In this work, we report the 1H, 15N and 13C NMR assignment of beech pollen Fag s 1 as well as the secondary structure information based on backbone chemical shifts. PMID:26289775

Resonance assignment of disordered protein with repetitive and overlapping sequence using combinatorial approach reveals initial structural propensities and local restrictions in the denatured state.

PubMed

Malik, Nikita; Kumar, Ashutosh

2016-09-01

NMR resonance assignment of intrinsically disordered proteins poses a challenge because of the limited dispersion of amide proton chemical shifts. This becomes even more complex with the increase in the size of the system. Residue specific selective labeling/unlabeling experiments have been used to resolve the overlap, but require multiple sample preparations. Here, we demonstrate an assignment strategy requiring only a single sample of uniformly labeled (13)C,(15)N-protein. We have used a combinatorial approach, involving 3D-HNN, CC(CO)NH and 2D-MUSIC, which allowed us to assign a denatured centromeric protein Cse4 of 229 residues. Further, we show that even the less sensitive experiments, when used in an efficient manner can lead to the complete assignment of a complex system without the use of specialized probes in a relatively short time frame. The assignment of the amino acids discloses the presence of local structural propensities even in the denatured state accompanied by restricted motion in certain regions that provides insights into the early folding events of the protein.

15N Hyperpolarization of Imidazole-15N2 for Magnetic Resonance pH Sensing via SABRE-SHEATH

PubMed Central

2016-01-01

15N nuclear spins of imidazole-15N2 were hyperpolarized using NMR signal amplification by reversible exchange in shield enables alignment transfer to heteronuclei (SABRE-SHEATH). A 15N NMR signal enhancement of ∼2000-fold at 9.4 T is reported using parahydrogen gas (∼50% para-) and ∼0.1 M imidazole-15N2 in methanol:aqueous buffer (∼1:1). Proton binding to a 15N site of imidazole occurs at physiological pH (pKa ∼ 7.0), and the binding event changes the 15N isotropic chemical shift by ∼30 ppm. These properties are ideal for in vivo pH sensing. Additionally, imidazoles have low toxicity and are readily incorporated into a wide range of biomolecules. 15N-Imidazole SABRE-SHEATH hyperpolarization potentially enables pH sensing on scales ranging from peptide and protein molecules to living organisms. PMID:27379344

15N Hyperpolarization of Imidazole-15N2 for Magnetic Resonance pH Sensing via SABRE-SHEATH.

PubMed

Shchepin, Roman V; Barskiy, Danila A; Coffey, Aaron M; Theis, Thomas; Shi, Fan; Warren, Warren S; Goodson, Boyd M; Chekmenev, Eduard Y

2016-06-24

15 N nuclear spins of imidazole- 15 N 2 were hyperpolarized using NMR signal amplification by reversible exchange in shield enables alignment transfer to heteronuclei (SABRE-SHEATH). A 15 N NMR signal enhancement of ∼2000-fold at 9.4 T is reported using parahydrogen gas (∼50% para-) and ∼0.1 M imidazole- 15 N 2 in methanol:aqueous buffer (∼1:1). Proton binding to a 15 N site of imidazole occurs at physiological pH (p K a ∼ 7.0), and the binding event changes the 15 N isotropic chemical shift by ∼30 ppm. These properties are ideal for in vivo pH sensing. Additionally, imidazoles have low toxicity and are readily incorporated into a wide range of biomolecules. 15 N-Imidazole SABRE-SHEATH hyperpolarization potentially enables pH sensing on scales ranging from peptide and protein molecules to living organisms.

AUTOBA: automation of backbone assignment from HN(C)N suite of experiments.

PubMed

Borkar, Aditi; Kumar, Dinesh; Hosur, Ramakrishna V

2011-07-01

Development of efficient strategies and automation represent important milestones of progress in rapid structure determination efforts in proteomics research. In this context, we present here an efficient algorithm named as AUTOBA (Automatic Backbone Assignment) designed to automate the assignment protocol based on HN(C)N suite of experiments. Depending upon the spectral dispersion, the user can record 2D or 3D versions of the experiments for assignment. The algorithm uses as inputs: (i) protein primary sequence and (ii) peak-lists from user defined HN(C)N suite of experiments. In the end, one gets H(N), (15)N, C(α) and C' assignments (in common BMRB format) for the individual residues along the polypeptide chain. The success of the algorithm has been demonstrated, not only with experimental spectra recorded on two small globular proteins: ubiquitin (76 aa) and M-crystallin (85 aa), but also with simulated spectra of 27 other proteins using assignment data from the BMRB.

Artifact suppression in electron paramagnetic resonance imaging of 14N- and 15N-labeled nitroxyl radicals with asymmetric absorption spectra

NASA Astrophysics Data System (ADS)

Takahashi, Wataru; Miyake, Yusuke; Hirata, Hiroshi

2014-10-01

This article describes an improved method for suppressing image artifacts in the visualization of 14N- and 15N-labeled nitroxyl radicals in a single image scan using electron paramagnetic resonance (EPR). The purpose of this work was to solve the problem of asymmetric EPR absorption spectra in spectral processing. A hybrid function of Gaussian and Lorentzian lineshapes was used to perform spectral line-fitting to successfully separate the two kinds of nitroxyl radicals. This approach can process the asymmetric EPR absorption spectra of the nitroxyl radicals being measured, and can suppress image artifacts due to spectral asymmetry. With this improved visualization method and a 750-MHz continuous-wave EPR imager, a temporal change in the distributions of a two-phase paraffin oil and water/glycerin solution system was visualized using lipophilic and hydrophilic nitroxyl radicals, i.e., 2-(14-carboxytetradecyl)-2-ethyl-4,4-dimethyl-3-oxazolidinyloxy (16-DOXYL stearic acid) and 4-hydroxyl-2,2,6,6-tetramethylpiperidine-d17-1-15N-1-oxyl (TEMPOL-d17-15N). The results of the two-phase separation experiment verified that reasonable artifact suppression could be achieved by the present method that deals with asymmetric absorption spectra in the EPR imaging of 14N- and 15N-labeled nitroxyl radicals.

Sequence-specific backbone resonance assignments and microsecond timescale molecular dynamics simulation of human eosinophil-derived neurotoxin.

PubMed

Gagné, Donald; Narayanan, Chitra; Bafna, Khushboo; Charest, Laurie-Anne; Agarwal, Pratul K; Doucet, Nicolas

2017-10-01

Eight active canonical members of the pancreatic-like ribonuclease A (RNase A) superfamily have been identified in human. All structural homologs share similar RNA-degrading functions, while also cumulating other various biological activities in different tissues. The functional homologs eosinophil-derived neurotoxin (EDN, or RNase 2) and eosinophil cationic protein (ECP, or RNase 3) are known to be expressed and secreted by eosinophils in response to infection, and have thus been postulated to play an important role in host defense and inflammatory response. We recently initiated the biophysical and dynamical investigation of several vertebrate RNase homologs and observed that clustering residue dynamics appear to be linked with the phylogeny and biological specificity of several members. Here we report the 1 H, 13 C and 15 N backbone resonance assignments of human EDN (RNase 2) and its molecular dynamics simulation on the microsecond timescale, providing means to pursue this comparative atomic-scale functional and dynamical analysis by NMR and computation over multiple time frames.

Proton nuclear magnetic resonance studies on the variant-3 neurotoxin from Centruroides sculpturatus Ewing: Sequential assignment of resonances

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nettesheim, D.G.; Klevit, R.E.; Drobny, G.

1989-02-21

The authors report the sequential assignment of resonances to specific residues in the proton nuclear magnetic resonance spectrum of the variant-3 neurotoxin from the scorpion Centruroides sculpturatus Ewing (range southwestern U.S.A.). A combination of two-dimensional NMR experiments such as 2D-COSY, 2D-NOESY, and single- and double-RELAY coherence transfer spectroscopy has been employed on samples of the protein dissolved in D{sub 2}O and in H{sub 2}O for assignment purposes. These studies provide a basis for the determination of the solution-phase conformation of this protein and for undertaking detailed structure-function studies of these neurotoxins that modulate the flow of sodium current by bindingmore » to the sodium channels of excitable membranes.« less

20 CFR 30.15 - May EEOICPA benefits be assigned, transferred or garnished?

Code of Federal Regulations, 2010 CFR

2010-04-01

... 20 Employees' Benefits 1 2010-04-01 2010-04-01 false May EEOICPA benefits be assigned, transferred or garnished? 30.15 Section 30.15 Employees' Benefits OFFICE OF WORKERS' COMPENSATION PROGRAMS... General Provisions Rights and Penalties § 30.15 May EEOICPA benefits be assigned, transferred or garnished...

Rapid NMR Assignments of Proteins by Using Optimized Combinatorial Selective Unlabeling.

PubMed

Dubey, Abhinav; Kadumuri, Rajashekar Varma; Jaipuria, Garima; Vadrevu, Ramakrishna; Atreya, Hanudatta S

2016-02-15

A new approach for rapid resonance assignments in proteins based on amino acid selective unlabeling is presented. The method involves choosing a set of multiple amino acid types for selective unlabeling and identifying specific tripeptides surrounding the labeled residues from specific 2D NMR spectra in a combinatorial manner. The methodology directly yields sequence specific assignments, without requiring a contiguously stretch of amino acid residues to be linked, and is applicable to deuterated proteins. We show that a 2D [(15) N,(1) H] HSQC spectrum with two 2D spectra can result in ∼50 % assignments. The methodology was applied to two proteins: an intrinsically disordered protein (12 kDa) and the 29 kDa (268 residue) α-subunit of Escherichia coli tryptophan synthase, which presents a challenging case with spectral overlaps and missing peaks. The method can augment existing approaches and will be useful for applications such as identifying active-site residues involved in ligand binding, phosphorylation, or protein-protein interactions, even prior to complete resonance assignments. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

32 CFR 150.15 - Assignments of error and briefs.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 32 National Defense 1 2012-07-01 2012-07-01 false Assignments of error and briefs. 150.15 Section 150.15 National Defense Department of Defense OFFICE OF THE SECRETARY OF DEFENSE REGULATIONS..., double-spaced on white paper, and securely fastened at the top. All references to matters contained in...

32 CFR 150.15 - Assignments of error and briefs.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 32 National Defense 1 2011-07-01 2011-07-01 false Assignments of error and briefs. 150.15 Section 150.15 National Defense Department of Defense OFFICE OF THE SECRETARY OF DEFENSE REGULATIONS..., double-spaced on white paper, and securely fastened at the top. All references to matters contained in...

32 CFR 150.15 - Assignments of error and briefs.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 32 National Defense 1 2010-07-01 2010-07-01 false Assignments of error and briefs. 150.15 Section 150.15 National Defense Department of Defense OFFICE OF THE SECRETARY OF DEFENSE REGULATIONS..., double-spaced on white paper, and securely fastened at the top. All references to matters contained in...

32 CFR 150.15 - Assignments of error and briefs.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 32 National Defense 1 2013-07-01 2013-07-01 false Assignments of error and briefs. 150.15 Section 150.15 National Defense Department of Defense OFFICE OF THE SECRETARY OF DEFENSE REGULATIONS..., double-spaced on white paper, and securely fastened at the top. All references to matters contained in...

Backbone and side-chain resonance assignments of (Ca2+)4-calmodulin bound to beta calcineurin A CaMBD peptide.

PubMed

Fowler, C Andrew; Núñez Hernandez, Maria F; O'Donnell, Susan E; Yu, Liping; Shea, Madeline A

2017-10-01

Calcineurin (CaN) is a heterodimeric and highly conserved serine/threonine phosphatase (PP2B) that plays a critical role in coupling calcium signals to physiological processes including embryonic cardiac development, NF-AT-regulated gene expression in immune responses, and apoptosis. The catalytic subunit (CaN A ) has three isoforms (α, β, and γ,) in humans and seven isoforms in Paramecium. In all eukaryotes, the EF-hand protein calmodulin (CaM) regulates CaN activity in a calcium-dependent manner. The N- and C-domains of CaM (CaM N and CaM C ) recognize a CaM-binding domain (CaMBD) within an intrinsically disordered region of CaN A that precedes the auto-inhibitory domain (AID) of CaN A . Here we present nearly complete 1 H, 13 C, and 15 N resonance assignments of (Ca 2+ ) 4 -CaM bound to a peptide containing the CaMBD sequence in the beta isoform of CaN A (βCaN A -CaMBDp). Its secondary structure elements predicted from the assigned chemical shifts were in good agreement with those observed in the high-resolution structures of (Ca 2+ ) 4 -CaM bound to CaMBDs of multiple enzymes. Based on the reported literature, the CaMBD of the α isoform of CaN A can bind to CaM in two opposing orientations which may influence the regulatory function of CaM. Because a high resolution structure of (Ca 2+ ) 4 -CaM bound to βCaN A -CaMBDp has not been reported, our studies serve as a starting point for determining the solution structure of this complex. This will demonstrate the preferred orientation of (Ca 2+ ) 4 -CaM on the CaMBD as well as the orientations of CaM N and CaM C relative to each other and to the AID of βCaN A .

Systematic assignment of Feshbach resonances via an asymptotic bound state model

NASA Astrophysics Data System (ADS)

Goosen, Maikel; Kokkelmans, Servaas

2008-05-01

We present an Asymptotic Bound state Model (ABM), which is useful to predict Feshbach resonances. The model utilizes asymptotic properties of the interaction potentials to represent coupled molecular wavefunctions. The bound states of this system give rise to Feshbach resonances, localized at the magnetic fields of intersection of these bound states with the scattering threshold. This model was very successful to assign measured Feshbach resonances in an ultra cold mixture of ^6Li and ^40K atomsootnotetextE. Wille, F.M. Spiegelhalder, G. Kerner, D. Naik, A. Trenkwalder, G. Hendl, F. Schreck, R. Grimm, T.G. Tiecke, J.T.M. Walraven, S.J.J.M.F. Kokkelmans, E. Tiesinga, P.S. Julienne, arXiv:0711.2916. For this system, the accuracy of the determined scattering lengths is comparable to full coupled channels results. However, it was not possible to predict the width of the resonances. We discuss how an incorporation of threshold effects will improve the model, and we apply it to a mixture of ^87Rb and ^133Cs atoms, where recently Feshbach resonances have been measured.

Three-Body Nature of N* and Δ* Resonances from Sequential Decay Chains

NASA Astrophysics Data System (ADS)

Thiel, A.; Sokhoyan, V.; Gutz, E.; van Pee, H.; Anisovich, A. V.; Bacelar, J. C. S.; Bantes, B.; Bartholomy, O.; Bayadilov, D.; Beck, R.; Beloglazov, Yu.; Castelijns, R.; Crede, V.; Dutz, H.; Elsner, D.; Ewald, R.; Frommberger, F.; Fuchs, M.; Funke, Ch.; Gregor, R.; Gridnev, A.; Hillert, W.; Hoffmeister, Ph.; Horn, I.; Jaegle, I.; Junkersfeld, J.; Kalinowsky, H.; Kammer, S.; Kleber, V.; Klein, Frank; Klein, Friedrich; Klempt, E.; Kotulla, M.; Krusche, B.; Lang, M.; Löhner, H.; Lopatin, I.; Lugert, S.; Mertens, T.; Messchendorp, J. G.; Metag, V.; Metsch, B.; Nanova, M.; Nikonov, V.; Novinski, D.; Novotny, R.; Ostrick, M.; Pant, L.; Pfeiffer, M.; Piontek, D.; Roy, A.; Sarantsev, A. V.; Schmidt, Ch.; Schmieden, H.; Shende, S.; Süle, A.; Sumachev, V. V.; Szczepanek, T.; Thoma, U.; Trnka, D.; Varma, R.; Walther, D.; Wendel, Ch.; Wilson, A.; Cbelsa/Taps Collaboration

2015-03-01

The N π0π0 decays of positive-parity N* and Δ* resonances at about 2 GeV are studied at ELSA by photoproduction of two neutral pions off protons. The data reveal clear evidence for several intermediate resonances: Δ (1232 ) , N (1520 )3 /2- , and N (1680 )5 /2+ , with spin parities JP=3 /2+ , 3 /2- , and 5 /2+. The partial wave analysis (within the Bonn-Gatchina approach) identifies N (1440 )1 /2+ and the N (π π )S wave (abbreviated as N σ here) as further isobars and assigns the final states to the formation of nucleon and Δ resonances and to nonresonant contributions. We observe the known Δ (1232 )π decays of Δ (1910 )1 /2+ , Δ (1920 )3 /2+, Δ (1905 )5 /2+, Δ (1950 )7 /2+, and of the corresponding spin-parity series in the nucleon sector, N (1880 )1 /2+, N (1900 )3 /2+, N (2000 )5 /2+, and N (1990 )7 /2+ . For the nucleon resonances, these decay modes are reported here for the first time. Further new decay modes proceed via N (1440 )1 /2+π , N (1520 )3 /2-π , N (1680 )5 /2+π , and N σ . The latter decay modes are observed in the decay of N* resonances and at most weakly in Δ* decays. It is argued that these decay modes provide evidence for a 3-quark nature of N* resonances rather than a quark-diquark structure.

Ratios of N15/C12 and He4/C12 inclusive electroproduction cross sections in the nucleon resonance region

NASA Astrophysics Data System (ADS)

Bosted, P. E.; Fersch, R.; Adams, G.; Amarian, M.; Anefalos, S.; Anghinolfi, M.; Asryan, G.; Avakian, H.; Bagdasaryan, H.; Baillie, N.; Ball, J. P.; Baltzell, N. A.; Barrow, S.; Batourine, V.; Battaglieri, M.; Beard, K.; Bedlinskiy, I.; Bektasoglu, M.; Bellis, M.; Benmouna, N.; Biselli, A. S.; Bonner, B. E.; Bouchigny, S.; Boiarinov, S.; Bradford, R.; Branford, D.; Brooks, W. K.; Bültmann, S.; Burkert, V. D.; Butuceanu, C.; Calarco, J. R.; Careccia, S. L.; Carman, D. S.; Carnahan, B.; Cazes, A.; Chen, S.; Cole, P. L.; Collins, P.; Coltharp, P.; Cords, D.; Corvisiero, P.; Crabb, D.; Crannell, H.; Crede, V.; Cummings, J. P.; de Masi, R.; de Vita, R.; de Sanctis, E.; Degtyarenko, P. V.; Denizli, H.; Dennis, L.; Deur, A.; Djalali, C.; Dodge, G. E.; Donnelly, J.; Doughty, D.; Dragovitsch, P.; Dugger, M.; Dharmawardane, K. V.; Dytman, S.; Dzyubak, O. P.; Egiyan, H.; Egiyan, K. S.; Elouadrhiri, L.; Eugenio, P.; Fatemi, R.; Fedotov, G.; Feuerbach, R. J.; Forest, T. A.; Fradi, A.; Funsten, H.; Garçon, M.; Gavalian, G.; Gilfoyle, G. P.; Giovanetti, K. L.; Girod, F. X.; Goetz, J. T.; Golovatch, E.; Gothe, R. W.; Griffioen, K. A.; Guidal, M.; Guillo, M.; Guler, N.; Guo, L.; Gyurjyan, V.; Hadjidakis, C.; Hafidi, K.; Hakobyan, R. S.; Hardie, J.; Heddle, D.; Hersman, F. W.; Hicks, K.; Hleiqawi, I.; Holtrop, M.; Huertas, M.; Hyde-Wright, C. E.; Ilieva, Y.; Ireland, D. G.; Ishkhanov, B. S.; Isupov, E. L.; Ito, M. M.; Jenkins, D.; Jo, H. S.; Joo, K.; Juengst, H. G.; Kalantarians, N.; Keith, C.; Kellie, J. D.; Khandaker, M.; Kim, K. Y.; Kim, K.; Kim, W.; Klein, A.; Klein, F. J.; Klusman, M.; Kossov, M.; Kramer, L. H.; Kubarovsky, V.; Kuhn, J.; Kuhn, S. E.; Kuleshov, S. V.; Lachniet, J.; Laget, J. M.; Langheinrich, J.; Lawrence, D.; Li, Ji; Lima, A. C. S.; Livingston, K.; Lu, H.; Lukashin, K.; MacCormick, M.; Markov, N.; McAleer, S.; McKinnon, B.; McNabb, J. W. C.; Mecking, B. A.; Mestayer, M. D.; Meyer, C. A.; Mibe, T.; Mikhailov, K.; Minehart, R.; Mirazita, M.; Miskimen, R.; Mokeev, V.; Morand, L.; Morrow, S. A.; Moteabbed, M.; Mueller, J.; Mutchler, G. S.; Nadel-Turonski, P.; Nasseripour, R.; Niccolai, S.; Niculescu, G.; Niculescu, I.; Niczyporuk, B. B.; Niroula, M. R.; Niyazov, R. A.; Nozar, M.; O'Rielly, G. V.; Osipenko, M.; Ostrovidov, A. I.; Park, K.; Pasyuk, E.; Paterson, C.; Philips, S. A.; Pierce, J.; Pivnyuk, N.; Pocanic, D.; Pogorelko, O.; Polli, E.; Pozdniakov, S.; Preedom, B. M.; Price, J. W.; Prok, Y.; Protopopescu, D.; Qin, L. M.; Raue, B. A.; Riccardi, G.; Ricco, G.; Ripani, M.; Rosner, G.; Rossi, P.; Rowntree, D.; Rubin, P. D.; Sabatié, F.; Salgado, C.; Santoro, J. P.; Sapunenko, V.; Schumacher, R. A.; Serov, V. S.; Sharabian, Y. G.; Shaw, J.; Shvedunov, N. V.; Skabelin, A. V.; Smith, E. S.; Smith, L. C.; Sober, D. I.; Stavinsky, A.; Stepanyan, S. S.; Stepanyan, S.; Stokes, B. E.; Stoler, P.; Strauch, S.; Suleiman, R.; Taiuti, M.; Taylor, S.; Tedeschi, D. J.; Thoma, U.; Tkabladze, A.; Tkachenko, S.; Todor, L.; Ungaro, M.; Vineyard, M. F.; Vlassov, A. V.; Weinstein, L. B.; Weygand, D. P.; Williams, M.; Wolin, E.; Wood, M. H.; Yegneswaran, A.; Yun, J.; Zana, L.; Zhang, J.; Zhao, B.; Zhao, Z.

2008-07-01

The (W,Q2) dependence of the ratio of inclusive electron scattering cross sections for N15/C12 was determined in the kinematic ranges 0.8resonance structure, in agreement with a simple phenomenological model and an extrapolation of deep-inelastic scattering ratios to low Q2. Ratios of He4/C12 using 1.6 to 2.5 GeV electrons were measured with very high statistical precision and were used to correct for He in the N and C targets. The (W,Q2) dependence of the He4/C12 ratios is in good agreement with that of the phenomenological model and exhibit significant resonance structure centered at W=0.94,1.23, and 1.5 GeV.

Amyloid Hydrogen Bonding Polymorphism Evaluated by (15)N{(17)O}REAPDOR Solid-State NMR and Ultra-High Resolution Fourier Transform Ion Cyclotron Resonance Mass Spectrometry.

PubMed

Wei, Juan; Antzutkin, Oleg N; Filippov, Andrei V; Iuga, Dinu; Lam, Pui Yiu; Barrow, Mark P; Dupree, Ray; Brown, Steven P; O'Connor, Peter B

2016-04-12

A combined approach, using Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) and solid-state NMR (Nuclear Magnetic Resonance), shows a high degree of polymorphism exhibited by Aβ species in forming hydrogen-bonded networks. Two Alzheimer's Aβ peptides, Ac-Aβ(16-22)-NH2 and Aβ(11-25), selectively labeled with (17)O and (15)N at specific amino acid residues were investigated. The total amount of peptides labeled with (17)O as measured by FTICR-MS enabled the interpretation of dephasing observed in (15)N{(17)O}REAPDOR solid-state NMR experiments. Specifically, about one-third of the Aβ peptides were found to be involved in the formation of a specific >C═(17)O···H-(15)N hydrogen bond with their neighbor peptide molecules, and we hypothesize that the rest of the molecules undergo ± n off-registry shifts in their hydrogen bonding networks.

Functional Single-Cell Approach to Probing Nitrogen-Fixing Bacteria in Soil Communities by Resonance Raman Spectroscopy with 15N2 Labeling.

PubMed

Cui, Li; Yang, Kai; Li, Hong-Zhe; Zhang, Han; Su, Jian-Qiang; Paraskevaidi, Maria; Martin, Francis L; Ren, Bin; Zhu, Yong-Guan

2018-04-17

Nitrogen (N) fixation is the conversion of inert nitrogen gas (N 2 ) to bioavailable N essential for all forms of life. N 2 -fixing microorganisms (diazotrophs), which play a key role in global N cycling, remain largely obscure because a large majority are uncultured. Direct probing of active diazotrophs in the environment is still a major challenge. Herein, a novel culture-independent single-cell approach combining resonance Raman (RR) spectroscopy with 15 N 2 stable isotope probing (SIP) was developed to discern N 2 -fixing bacteria in a complex soil community. Strong RR signals of cytochrome c (Cyt c, frequently present in diverse N 2 -fixing bacteria), along with a marked 15 N 2 -induced Cyt c band shift, generated a highly distinguishable biomarker for N 2 fixation. 15 N 2 -induced shift was consistent well with 15 N abundance in cell determined by isotope ratio mass spectroscopy. By applying this biomarker and Raman imaging, N 2 -fixing bacteria in both artificial and complex soil communities were discerned and imaged at the single-cell level. The linear band shift of Cyt c versus 15 N 2 percentage allowed quantification of N 2 fixation extent of diverse soil bacteria. This single-cell approach will advance the exploration of hitherto uncultured diazotrophs in diverse ecosystems.

1H, 13C and 15N assignment of the C-terminal domain of GNA2132 from Neisseria meningitidis

PubMed Central

Esposito, Veronica; Musi, Valeria; Veggi, Daniele; Pizza, Mariagrazia

2010-01-01

GNA2132 (Genome-derived Neisseria Antigen 2132) is a surface-exposed lipoprotein discovered by reverse vaccinology and expressed by genetically diverse Neisseria meningitidis strains (Pizza et al. 2000). The protein induces bactericidal antibodies against most strains of Meningococccus and has been included in a multivalent recombinant vaccine against N. meningitidis serogroup B. Structure determination of GNA2132 is important for understanding the antigenic properties of the protein in view of increased efficiency vaccine development. We report practically complete 1H, 13C and 15N assignment of the detectable spectrum of a highly conserved C-terminal region of GNA2132 (residues 245–427) in micellar solution, a medium used to improve the spectral quality. The first 32 residues of our construct up to residue 277 were not visible in the spectrum, presumably because of line broadening due to solvent and/or conformational exchange. Secondary structure predictions based on chemical shift information indicate the presence of an all β-protein with eight β strands. PMID:20300890

1H, 13C and 15N assignment of the C-terminal domain of GNA2132 from Neisseria meningitidis.

PubMed

Esposito, Veronica; Musi, Valeria; Veggi, Daniele; Pastore, Annalisa; Pizza, Mariagrazia

2010-04-01

GNA2132 (Genome-derived Neisseria Antigen 2132) is a surface-exposed lipoprotein discovered by reverse vaccinology and expressed by genetically diverse Neisseria meningitidis strains (Pizza et al. 2000). The protein induces bactericidal antibodies against most strains of Meningococccus and has been included in a multivalent recombinant vaccine against N. meningitidis serogroup B. Structure determination of GNA2132 is important for understanding the antigenic properties of the protein in view of increased efficiency vaccine development. We report practically complete (1)H, (13)C and (15)N assignment of the detectable spectrum of a highly conserved C-terminal region of GNA2132 (residues 245-427) in micellar solution, a medium used to improve the spectral quality. The first 32 residues of our construct up to residue 277 were not visible in the spectrum, presumably because of line broadening due to solvent and/or conformational exchange. Secondary structure predictions based on chemical shift information indicate the presence of an all beta-protein with eight beta strands.

1H and 15N NMR resonance assignments and secondary structure of titin type I domains.

PubMed

Muhle-Goll, C; Nilges, M; Pastore, A

1997-01-01

Titin/connectin is a giant muscle protein with a highly modular architecture consisting of multiple repeats of two sequence motifs, named type I and type II. Type I modules have been suggested to be intracellular members of the fibronectin type III (Fn3) domain family. Along the titin sequence they are exclusively present in the region of the molecule located in the sarcomere A-band. This region has been shown to interact with myosin and C-protein. One of the most noticeable features of type I modules is that they are particularly rich in semiconserved prolines, since these residues account for about 8% of their sequence. We have determined the secondary structure of a representative type I domain (A71) by 15N and 1H NMR. We show that the type I domains of titin have the Fn3 fold as proposed, consisting of a three- and a four-stranded beta-sheet. When the two sheets are placed on top of each other to form the beta-sandwich characteristic of the Fn3 fold, 8 out of 10 prolines are found on the same side of the molecule and form an exposed hydrophobic patch. This suggests that the semiconserved prolines might be relevant for the function of type I modules, providing a surface for binding to other A-band proteins. The secondary structure of A71 was structurally aligned to other extracellular Fn3 modules of known 3D structure. The alignment shows that titin type I modules have closest similarity to the first Fn3 domain of Drosophila neuroglian.

Fast and accurate resonance assignment of small-to-large proteins by combining automated and manual approaches.

PubMed

Niklasson, Markus; Ahlner, Alexandra; Andresen, Cecilia; Marsh, Joseph A; Lundström, Patrik

2015-01-01

The process of resonance assignment is fundamental to most NMR studies of protein structure and dynamics. Unfortunately, the manual assignment of residues is tedious and time-consuming, and can represent a significant bottleneck for further characterization. Furthermore, while automated approaches have been developed, they are often limited in their accuracy, particularly for larger proteins. Here, we address this by introducing the software COMPASS, which, by combining automated resonance assignment with manual intervention, is able to achieve accuracy approaching that from manual assignments at greatly accelerated speeds. Moreover, by including the option to compensate for isotope shift effects in deuterated proteins, COMPASS is far more accurate for larger proteins than existing automated methods. COMPASS is an open-source project licensed under GNU General Public License and is available for download from http://www.liu.se/forskning/foass/tidigare-foass/patrik-lundstrom/software?l=en. Source code and binaries for Linux, Mac OS X and Microsoft Windows are available.

Fast and Accurate Resonance Assignment of Small-to-Large Proteins by Combining Automated and Manual Approaches

PubMed Central

Niklasson, Markus; Ahlner, Alexandra; Andresen, Cecilia; Marsh, Joseph A.; Lundström, Patrik

2015-01-01

The process of resonance assignment is fundamental to most NMR studies of protein structure and dynamics. Unfortunately, the manual assignment of residues is tedious and time-consuming, and can represent a significant bottleneck for further characterization. Furthermore, while automated approaches have been developed, they are often limited in their accuracy, particularly for larger proteins. Here, we address this by introducing the software COMPASS, which, by combining automated resonance assignment with manual intervention, is able to achieve accuracy approaching that from manual assignments at greatly accelerated speeds. Moreover, by including the option to compensate for isotope shift effects in deuterated proteins, COMPASS is far more accurate for larger proteins than existing automated methods. COMPASS is an open-source project licensed under GNU General Public License and is available for download from http://www.liu.se/forskning/foass/tidigare-foass/patrik-lundstrom/software?l=en. Source code and binaries for Linux, Mac OS X and Microsoft Windows are available. PMID:25569628

Infrared spectra and anharmonic coupling of proton-bound nitrogen dimers N2-H+-N2, N2-D+-N2, and 15N2-H+-15N2 in solid para-hydrogen.

PubMed

Liao, Hsin-Yi; Tsuge, Masashi; Tan, Jake A; Kuo, Jer-Lai; Lee, Yuan-Pern

2017-08-09

The proton-bound nitrogen dimer, N 2 -H + -N 2 , and its isotopologues were investigated by means of vibrational spectroscopy. These species were produced upon electron bombardment of mixtures of N 2 (or 15 N 2 ) and para-hydrogen (p-H 2 ) or normal-D 2 (n-D 2 ) during deposition at 3.2 K. Reduced-dimension anharmonic vibrational Schrödinger equations were constructed to account for the strong anharmonic effects in these protonated species. The fundamental lines of proton motions in N 2 -H + -N 2 were observed at 715.0 (NH + N antisymmetric stretch, ν 4 ), 1129.6 (NH + N bend, ν 6 ), and 2352.7 (antisymmetric NN/NN stretch, ν 3 ) cm -1 , in agreement with values of 763, 1144, and 2423 cm -1 predicted with anharmonic calculations using the discrete-variable representation (DVR) method at the CCSD/aug-cc-pVDZ level. The lines at 1030.2 and 1395.5 cm -1 were assigned to combination bands involving nν 2 + ν 4 (n = 1 and 2) according to theoretical calculations; ν 2 is the N 2 N 2 stretching mode. For 15 N 2 -H + - 15 N 2 in solid p-H 2 , the corresponding major lines were observed at 710.0 (ν 4 ), 1016.7 (ν 2 + ν 4 ), 1124.3 (ν 6 ), 1384.8 (2ν 2 + ν 4 ), and 2274.9 (ν 3 ) cm -1 . For N 2 -D + -N 2 in solid n-D 2 , the corresponding major lines were observed at 494.0 (ν 4 ), 840.7 (ν 2 + ν 4 ), 825.5 (ν 6 ), and 2356.2 (ν 3 ) cm -1 . In addition, two lines at 762.0 (weak) and 808.3 cm -1 were tentatively assigned to be some modes of N 2 -H + -N 2 perturbed or activated by a third N 2 near the proton.

Backbone dynamics of a model membrane protein: assignment of the carbonyl carbon /sup 13/C NMR resonances in detergent-solubilized M13 coat protein

DOE Office of Scientific and Technical Information (OSTI.GOV)

Henry, G.D.; Weiner, J.H.; Sykes, B.D.

The major coat protein of the filamentous bacteriophage M13 is a 50-residue amphiphilic polypeptide which is inserted, as an integral membrane-spanning protein, in the inner membrane of the Escherichia coli host during infection. /sup 13/C was incorporated biosynthetically into a total of 23 of the peptide carbonyls using labeled amino acids (alanine, glycine, lysine, phenylalanine, and proline). The structure and dynamics of carbonyl-labeled M13 coat protein were monitored by /sup 13/C nuclear magnetic resonance (NMR) spectroscopy. Assignment of many resonances was achieved by using protease digestion, pH titration, or labeling of the peptide bond with both /sup 13/C and /supmore » 15/N. The carbonyl region of the natural-abundance /sup 13/C NMR spectrum of M13 coat protein in sodium dodecyl sulfate solution shows approximately eight backbone carbonyl resonances with line widths much narrower than the rest. Three of these more mobile residues correspond to assigned peaks (glycine-3, lysine-48, and alanine-49) in the individual amino acid spectra, and another almost certainly arises from glutamic acid-2. A ninth residue, alanine-1, also gives rise to a very narrow carbonyl resonance if the pH is well above or below the pK/sub a/ of the terminal amino group. These data suggest that only about four residues at either end of the protein experience large-amplitude spatial fluctuations; the rest of the molecule is essentially rigid on the time scale of the overall rotational tumbling of the protein-detergent complex. The relative exposure of different regions of detergent-bound protein was monitored by limited digestion with proteinase K. Comparable spectra and digestion patterns were obtained when the protein was solubilized in sodium deoxycholate, suggesting that the coat protein binds both amphiphiles in a similar fashion.« less

Rapid analysis of protein backbone resonance assignments using cryogenic probes, a distributed Linux-based computing architecture, and an integrated set of spectral analysis tools.

PubMed

Monleón, Daniel; Colson, Kimberly; Moseley, Hunter N B; Anklin, Clemens; Oswald, Robert; Szyperski, Thomas; Montelione, Gaetano T

2002-01-01

Rapid data collection, spectral referencing, processing by time domain deconvolution, peak picking and editing, and assignment of NMR spectra are necessary components of any efficient integrated system for protein NMR structure analysis. We have developed a set of software tools designated AutoProc, AutoPeak, and AutoAssign, which function together with the data processing and peak-picking programs NMRPipe and Sparky, to provide an integrated software system for rapid analysis of protein backbone resonance assignments. In this paper we demonstrate that these tools, together with high-sensitivity triple resonance NMR cryoprobes for data collection and a Linux-based computer cluster architecture, can be combined to provide nearly complete backbone resonance assignments and secondary structures (based on chemical shift data) for a 59-residue protein in less than 30 hours of data collection and processing time. In this optimum case of a small protein providing excellent spectra, extensive backbone resonance assignments could also be obtained using less than 6 hours of data collection and processing time. These results demonstrate the feasibility of high throughput triple resonance NMR for determining resonance assignments and secondary structures of small proteins, and the potential for applying NMR in large scale structural proteomics projects.

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Backbone resonance assignments of complexes of human voltage-dependent sodium channel NaV1.2 IQ motif peptide bound to apo calmodulin and to the C-domain fragment of apo calmodulin.

PubMed

Mahling, Ryan; Kilpatrick, Adina M; Shea, Madeline A

2017-10-01

Human voltage-gated sodium channel Na V 1.2 has a single pore-forming α-subunit and two transmembrane β-subunits. Expressed primarily in the brain, Na V 1.2 is critical for initiation and propagation of action potentials. Milliseconds after the pore opens, sodium influx is terminated by inactivation processes mediated by regulatory proteins including calmodulin (CaM). Both calcium-free (apo) CaM and calcium-saturated CaM bind tightly to an IQ motif in the C-terminal tail of the α-subunit. Our thermodynamic studies and solution structure (2KXW) of a C-domain fragment of apo 13 C, 15 N- CaM (CaM C ) bound to an unlabeled peptide with the sequence of rat Na V 1.2 IQ motif showed that apo CaM C (a) was necessary and sufficient for binding, and (b) bound more favorably than calcium-saturated CaM C . However, we could not monitor the Na V 1.2 residues directly, and no structure of full-length CaM (including the N-domain of CaM (CaM N )) was determined. To distinguish contributions of CaM N and CaM C , we used solution NMR spectroscopy to assign the backbone resonances of a complex containing a 13 C, 15 N-labeled peptide with the sequence of human Na V 1.2 IQ motif (Na V 1.2 IQp ) bound to apo 13 C, 15 N-CaM or apo 13 C, 15 N-CaM C . Comparing the assignments of apo CaM in complex with Na V 1.2 IQp to those of free apo CaM showed that residues within CaM C were significantly perturbed, while residues within CaM N were essentially unchanged. The chemical shifts of residues in Na V 1.2 IQp and in the C-domain of CaM were nearly identical regardless of whether CaM N was covalently linked to CaM C . This suggests that CaM N does not influence apo CaM binding to Na V 1.2 IQp .

15N and13C NMR investigation of hydroxylamine-derivatized humic substances

USGS Publications Warehouse

Thorn, K.A.; Arterburn, J.B.; Mikita, M.A.

1992-01-01

Five fulvic and humic acid samples of diverse origins were derivatized with 15N-labeled hydroxylamine and analyzed by liquid-phase 15N NMR spectrometry. The 15N NMR spectra indicated that hydroxylamine reacted similarly with all samples and could discriminate among carbonyl functional groups. Oximes were the major derivatives; resonances attributable to hydroxamic acids, the reaction products of hydroxylamine with esters, and resonances attributable to the tautomeric equilibrium position between the nitrosophenol and monoxime derivatives of quinones, the first direct spectroscopic evidence for quinones, also were evident. The 15N NMR spectra also suggested the presence of nitriles, oxazoles, oxazolines, isocyanides, amides, and lactams, which may all be explained in terms of Beckmann reactions of the initial oxime derivatives. INEPT and ACOUSTIC 15N NMR spectra provided complementary information on the derivatized samples. 13C NMR spectra of derivatized samples indicated that the ketone/quinone functionality is incompletely derivatized with hydroxylamine. ?? 1991 American Chemical Society.

Selective excitation enables assignment of proton resonances and (1)H-(1)H distance measurement in ultrafast magic angle spinning solid state NMR spectroscopy.

PubMed

Zhang, Rongchun; Ramamoorthy, Ayyalusamy

2015-07-21

Remarkable developments in ultrafast magic angle spinning (MAS) solid-state NMR spectroscopy enabled proton-based high-resolution multidimensional experiments on solids. To fully utilize the benefits rendered by proton-based ultrafast MAS experiments, assignment of (1)H resonances becomes absolutely necessary. Herein, we propose an approach to identify different proton peaks by using dipolar-coupled heteronuclei such as (13)C or (15)N. In this method, after the initial preparation of proton magnetization and cross-polarization to (13)C nuclei, transverse magnetization of desired (13)C nuclei is selectively prepared by using DANTE (Delays Alternating with Nutations for Tailored Excitation) sequence and then, it is transferred to bonded protons with a short-contact-time cross polarization. Our experimental results demonstrate that protons bonded to specific (13)C atoms can be identified and overlapping proton peaks can also be assigned. In contrast to the regular 2D HETCOR experiment, only a few 1D experiments are required for the complete assignment of peaks in the proton spectrum. Furthermore, the finite-pulse radio frequency driven recoupling sequence could be incorporated right after the selection of specific proton signals to monitor the intensity buildup for other proton signals. This enables the extraction of (1)H-(1)H distances between different pairs of protons. Therefore, we believe that the proposed method will greatly aid in fast assignment of peaks in proton spectra and will be useful in the development of proton-based multi-dimensional solid-state NMR experiments to study atomic-level resolution structure and dynamics of solids.

Nuclear resonance vibrational spectroscopy applied to [Fe(OEP)(NO)]: the vibrational assignments of five-coordinate ferrous heme-nitrosyls and implications for electronic structure.

PubMed

Lehnert, Nicolai; Galinato, Mary Grace I; Paulat, Florian; Richter-Addo, George B; Sturhahn, Wolfgang; Xu, Nan; Zhao, Jiyong

2010-05-03

This study presents Nuclear Resonance Vibrational Spectroscopy (NRVS) data on the five-coordinate (5C) ferrous heme-nitrosyl complex [Fe(OEP)(NO)] (1, OEP(2-) = octaethylporphyrinato dianion) and the corresponding (15)N(18)O labeled complex. The obtained spectra identify two isotope sensitive features at 522 and 388 cm(-1), which shift to 508 and 381 cm(-1), respectively, upon isotope labeling. These features are assigned to the Fe-NO stretch nu(Fe-NO) and the in-plane Fe-N-O bending mode delta(ip)(Fe-N-O), the latter has been unambiguously assigned for the first time for 1. The obtained NRVS data were simulated using our quantum chemistry centered normal coordinate analysis (QCC-NCA). Since complex 1 can potentially exist in 12 different conformations involving the FeNO and peripheral ethyl orientations, extended density functional theory (DFT) calculations and QCC-NCA simulations were performed to determine how these conformations affect the NRVS properties of [Fe(OEP)NO]. These results show that the properties and force constants of the FeNO unit are hardly affected by the conformational changes involving the ethyl substituents. On the other hand, the NRVS-active porphyrin-based vibrations around 340-360, 300-320, and 250-270 cm(-1) are sensitive to the conformational changes. The spectroscopic changes observed in these regions are due to selective mechanical couplings of one component of E(u)-type (in ideal D(4h) symmetry) porphyrin-based vibrations with the in-plane Fe-N-O bending mode. This leads to the observed variations in Fe(OEP) core mode energies and NRVS intensities without affecting the properties of the FeNO unit. The QCC-NCA simulated NRVS spectra of 1 show excellent agreement with experiment, and indicate that conformer F is likely present in the samples of this complex investigated here. The observed porphyrin-based vibrations in the NRVS spectra of 1 are also assigned based on the QCC-NCA results. The obtained force constants of the Fe-NO and N

15N nuclear magnetic resonance studies on the tautomerism of 8-hydroxy-2'-deoxyguanosine, 8-hydroxyguanosine, and other C8-substituted guanine nucleosides.

PubMed

Cho, B P; Kadlubar, F F; Culp, S J; Evans, F E

1990-01-01

The favored tautomeric and ionic structures were examined for the oxidative DNA damage adduct 8-hydroxy-2'-deoxyguanosine and its RNA analogue 8-hydroxyguanosine by 15N NMR spectroscopy. In addition, 15N chemical shifts and coupling constants from 13 different guanine nucleosides, including a wide variety of C8 substitutions (OH, SH, Br, OCH2C6H5, OCH3, SCH3, and SO2CH3), have been analyzed with respect to their tautomeric structures. A -98.5-Hz proton-nitrogen coupling constant observed for the N7 resonance of 8-hydroxyguanosine in dimethyl sulfoxide was evidence for 8-keto substitution, which is contrary to the structure implied by the generally used nomenclature. The pH dependence of 15N NMR spectra of 8-hydroxyguanosine in aqueous solution showed downfield shifts of the N1 and N7 resonances that were greater than 50 ppm, which indicated the conversion from a neutral 6,8-diketo to a 6-enolate-8-keto (pKa1 = 8.6) and finally to a 6,8-dienolate structure (pKa2 = 11.7). There was no evidence of an 8-enol substituent in the absence of ionization. It is proposed that the syn conformation of these oxidized bases in duplex DNA and RNA can be further stabilized by abnormal hydrogen bonding or mispairing that involves N7-H. The combined data show that 15N NMR is a sensitive probe to examine tautomerism of the guanine ring system. The analysis indicates that the change from a single to a double bond for the C8 substituent, and the accompanying removal of the normal double bond between N7 and C8 on the imidazole ring system, has no detectable effect on the tautomerism at the N1-O6 site of the pyrimidine ring system for both the 8-keto and 8-thio substitutions. In addition, large differences in electronegativity of the C8 substituents do not alter the N1-O6 tautomerism.

Electro-optic guided-mode resonance tuning suppressible by optically induced screening in a vertically coupled hybrid GaN/Si microring resonator

NASA Astrophysics Data System (ADS)

Thubthimthong, B.; Sasaki, T.; Hane, K.

2018-02-01

GaN as a nanophotonic material has gained much attention in recent years. Using the hybrid GaN/Si platform, we report the electro-optic tuning of guided-mode resonance in a vertically coupled hybrid GaN/Si microring resonator operating in the 1.5 μm window with up to a 6 dB extinction ratio and a 1.5 MHz modulation frequency (test equipment limit). The electro-optic tuning could be optically suppressed by electron-hole-originated screening induced by an ultraviolet excitation at 325 nm. Our work may benefit in externally intervenable optical interconnects for uninterrupted secure photonic networks.

Novel Peak Assignments of in Vivo 13C MRS in Human Brain at 1.5 T

NASA Astrophysics Data System (ADS)

Blüml, Stefan; Hwang, Jong-Hee; Moreno, Angel; Ross, Brian D.

2000-04-01

13C MRS studies at natural abundance and after intravenous 1-13C glucose infusion were performed on a 1.5-T clinical scanner in four subjects. Localization to the occipital cortex was achieved by a surface coil. In natural abundance spectra glucose C3β,5β, myo-inositol, glutamate C1,2,5, glutamine C1,2,5, N-acetyl-aspartate C1-4,Cdbnd O, creatine CH2, CH3, and CCdbnd N, taurine C2,3, bicarbonate HCO-3 were identified. After glucose infusion 13C enrichment of glucose C1α,1β, glutamate C1-4, glutamine C1-4, aspartate C2,3, N-acetyl-aspartate C2,3, lactate C3, alanine C3, and HCO-3 were observed. The observation of 13C enrichment of resonances resonating at >150 ppm is an extension of previously published studies and will provide a more precise determination of metabolic rates and substrate decarboxylation in human brain.

Cross sections for n+{sup 14}N from an R-matrix analysis of the {sup 15}N system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hale, G.M.; Young, P.G.; Chadwick, M.B.

1994-06-01

As part of the Hiroshima-Nagasaki Dose Reevaluation Program, a new evaluation of the neutron cross sections for {sup 14}N was made for ENDF/B-VI, based at energies below 2.5 MeV on a multichannel R-matrix analysis of reactions in the {sup 15}N system. The types of data used in the analysis, and the resulting cross sections and resonance structure for {sup 15}N are briefly described. The resonant features of the neutron cross sections were especially well determined by including precise, high-resolution neutron total cross section measurements from ORNL. While the new evaluated cross section appear to be significant improvements over the earliermore » ones, they still need to be tested more extensively against recent measurements of the differential elastic cross section from Oak Ridge.« less

Using 15N-Ammonium to Characterise and Map Potassium Binding Sites in Proteins by NMR Spectroscopy

PubMed Central

Werbeck, Nicolas D; Kirkpatrick, John; Reinstein, Jochen; Hansen, D Flemming

2014-01-01

A variety of enzymes are activated by the binding of potassium ions. The potassium binding sites of these enzymes are very specific, but ammonium ions can often replace potassium ions in vitro because of their similar ionic radii. In these cases, ammonium can be used as a proxy for potassium to characterise potassium binding sites in enzymes: the 1H,15N spin-pair of enzyme-bound 15NH4+ can be probed by 15N-edited heteronuclear NMR experiments. Here, we demonstrate the use of NMR spectroscopy to characterise binding of ammonium ions to two different enzymes: human histone deacetylase 8 (HDAC8), which is activated allosterically by potassium, and the bacterial Hsp70 homologue DnaK, for which potassium is an integral part of the active site. Ammonium activates both enzymes in a similar way to potassium, thus supporting this non-invasive approach. Furthermore, we present an approach to map the observed binding site onto the structure of HDAC8. Our method for mapping the binding site is general and does not require chemical shift assignment of the enzyme resonances. PMID:24520048

An efficient randomized algorithm for contact-based NMR backbone resonance assignment.

PubMed

Kamisetty, Hetunandan; Bailey-Kellogg, Chris; Pandurangan, Gopal

2006-01-15

Backbone resonance assignment is a critical bottleneck in studies of protein structure, dynamics and interactions by nuclear magnetic resonance (NMR) spectroscopy. A minimalist approach to assignment, which we call 'contact-based', seeks to dramatically reduce experimental time and expense by replacing the standard suite of through-bond experiments with the through-space (nuclear Overhauser enhancement spectroscopy, NOESY) experiment. In the contact-based approach, spectral data are represented in a graph with vertices for putative residues (of unknown relation to the primary sequence) and edges for hypothesized NOESY interactions, such that observed spectral peaks could be explained if the residues were 'close enough'. Due to experimental ambiguity, several incorrect edges can be hypothesized for each spectral peak. An assignment is derived by identifying consistent patterns of edges (e.g. for alpha-helices and beta-sheets) within a graph and by mapping the vertices to the primary sequence. The key algorithmic challenge is to be able to uncover these patterns even when they are obscured by significant noise. This paper develops, analyzes and applies a novel algorithm for the identification of polytopes representing consistent patterns of edges in a corrupted NOESY graph. Our randomized algorithm aggregates simplices into polytopes and fixes inconsistencies with simple local modifications, called rotations, that maintain most of the structure already uncovered. In characterizing the effects of experimental noise, we employ an NMR-specific random graph model in proving that our algorithm gives optimal performance in expected polynomial time, even when the input graph is significantly corrupted. We confirm this analysis in simulation studies with graphs corrupted by up to 500% noise. Finally, we demonstrate the practical application of the algorithm on several experimental beta-sheet datasets. Our approach is able to eliminate a large majority of noise edges and to

The N+CPT resonance

NASA Astrophysics Data System (ADS)

Crescimanno, Michael; Hohensee, Michael; Hancox, Cindy; Phillips, David; Walsworth, Ron

2007-06-01

Of relevance to compact atomic frequency standards, we investigate a model of the N+CPT joint optical resonance. We compare analytical solutions of a 4-state theory, as well as numerical solutions of the optical Bloch equations, to experimental investigations of N+CPT resonances in 87Rb. Our results inform the optimization of N+CPT based frequency standards.

Complete NMR assignment of a bisecting hybrid-type oligosaccharide transferred by Mucor hiemalis endo-β-N-acetylglucosaminidase.

PubMed

Yamanoi, Takashi; Oda, Yoshiki; Katsuraya, Kaname; Inazu, Toshiyuki; Yamamoto, Kenji

2016-06-02

This study describes the complete nuclear magnetic resonance (NMR) spectral assignment of a bisecting hybrid-type oligosaccharide 1, transferred by Mucor hiemalis endo-β-N-acetylglucosaminidase (Endo-M). Through (1)H- and (13)C-NMR, DQF-COSY, HSQC, HMBC, TOCSY, and NOESY experiments, we determine the structure of the glycoside linkage formed by the Endo-M transglycosylation, i.e., the connection between GlcNAc and GlcNAc in oligosaccharide 1. Copyright © 2016 Elsevier Ltd. All rights reserved.

Backbone ¹H, ¹³C, ¹⁵N NMR assignments of yeast OMP synthase in unliganded form and in complex with orotidine 5'-monophosphate.

PubMed

Hansen, Michael Riis; Harris, Richard; Barr, Eric W; Cheng, Hong; Girvin, Mark E; Grubmeyer, Charles

2014-04-01

The type I phosphoribosyltransferase OMP synthase (EC 2.4.2.10) is involved in de novo synthesis of pyrimidine nucleotides forming the UMP precursor orotidine 5'-monophosphate (OMP). The homodimeric enzyme has a Rossman α/β core topped by a base-enclosing "hood" domain and a flexible domain-swapped catalytic loop. High-resolution X-ray structures of the homologous Salmonella typhimurium and yeast enzymes show that a general compacting of the core as well as movement of the hood and a major disorder-to-order transition of the loop occur upon binding of ligands MgPRPP and orotate. Here we present backbone NMR assignments for the unliganded yeast enzyme (49 kDa) and its complex with product OMP. We were able to assign 212-213 of the 225 non-proline backbone (15)N and amide proton resonances. Significant difference in chemical shifts of the amide cross peaks occur in regions of the structure that undergo movement upon ligand occupancy in the S. typhimurium enzyme.

Spin injection in n-type resonant tunneling diodes.

PubMed

Orsi Gordo, Vanessa; Herval, Leonilson Ks; Galeti, Helder Va; Gobato, Yara Galvão; Brasil, Maria Jsp; Marques, Gilmar E; Henini, Mohamed; Airey, Robert J

2012-10-25

We have studied the polarized resolved photoluminescence of n-type GaAs/AlAs/GaAlAs resonant tunneling diodes under magnetic field parallel to the tunnel current. Under resonant tunneling conditions, we have observed two emission lines attributed to neutral (X) and negatively charged excitons (X-). We have observed a voltage-controlled circular polarization degree from the quantum well emission for both lines, with values up to -88% at 15 T at low voltages which are ascribed to an efficient spin injection from the 2D gases formed at the accumulation layers.

Characterization of Nylon 6 by 15N Solid State NMR

DTIC Science & Technology

1989-05-31

M.; Ritchey, W.; de Boer, E. Macromolecules, 1979, 12, 924. 2. Garroway , A. N.; Ritchey, W. M.; Moniz, W. B.; Macromolecules, 1982, It, 1051. 3...E. Macromolecules, 1982, 15, 1406. 23. Veeman, W. S.; Menger, E. M. Bull. Magn. Reson., 1980,2,77. 24. VanderHart, D. L.; Garroway , A. N. J. Chem

Practical aspects of NMR signal assignment in larger and challenging proteins

PubMed Central

Frueh, Dominique P.

2014-01-01

NMR has matured into a technique routinely employed for studying proteins in near physiological conditions. However, applications to larger proteins are impeded by the complexity of the various correlation maps necessary to assign NMR signals. This article reviews the data analysis techniques traditionally employed for resonance assignment and describes alternative protocols necessary for overcoming challenges in large protein spectra. In particular, simultaneous analysis of multiple spectra may help overcome ambiguities or may reveal correlations in an indirect manner. Similarly, visualization of orthogonal planes in a multidimensional spectrum can provide alternative assignment procedures. We describe examples of such strategies for assignment of backbone, methyl, and nOe resonances. We describe experimental aspects of data acquisition for the related experiments and provide guidelines for preliminary studies. Focus is placed on large folded monomeric proteins and examples are provided for 37, 48, 53, and 81 kDa proteins. PMID:24534088

Selective excitation enables assignment of proton resonances and {sup 1}H-{sup 1}H distance measurement in ultrafast magic angle spinning solid state NMR spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Rongchun; Ramamoorthy, Ayyalusamy, E-mail: ramamoor@umich.edu

2015-07-21

Remarkable developments in ultrafast magic angle spinning (MAS) solid-state NMR spectroscopy enabled proton-based high-resolution multidimensional experiments on solids. To fully utilize the benefits rendered by proton-based ultrafast MAS experiments, assignment of {sup 1}H resonances becomes absolutely necessary. Herein, we propose an approach to identify different proton peaks by using dipolar-coupled heteronuclei such as {sup 13}C or {sup 15}N. In this method, after the initial preparation of proton magnetization and cross-polarization to {sup 13}C nuclei, transverse magnetization of desired {sup 13}C nuclei is selectively prepared by using DANTE (Delays Alternating with Nutations for Tailored Excitation) sequence and then, it is transferredmore » to bonded protons with a short-contact-time cross polarization. Our experimental results demonstrate that protons bonded to specific {sup 13}C atoms can be identified and overlapping proton peaks can also be assigned. In contrast to the regular 2D HETCOR experiment, only a few 1D experiments are required for the complete assignment of peaks in the proton spectrum. Furthermore, the finite-pulse radio frequency driven recoupling sequence could be incorporated right after the selection of specific proton signals to monitor the intensity buildup for other proton signals. This enables the extraction of {sup 1}H-{sup 1}H distances between different pairs of protons. Therefore, we believe that the proposed method will greatly aid in fast assignment of peaks in proton spectra and will be useful in the development of proton-based multi-dimensional solid-state NMR experiments to study atomic-level resolution structure and dynamics of solids.« less

Spin injection in n-type resonant tunneling diodes

PubMed Central

2012-01-01

We have studied the polarized resolved photoluminescence of n-type GaAs/AlAs/GaAlAs resonant tunneling diodes under magnetic field parallel to the tunnel current. Under resonant tunneling conditions, we have observed two emission lines attributed to neutral (X) and negatively charged excitons (X−). We have observed a voltage-controlled circular polarization degree from the quantum well emission for both lines, with values up to −88% at 15 T at low voltages which are ascribed to an efficient spin injection from the 2D gases formed at the accumulation layers. PMID:23098559

Iron-Rhodium and Iron-Iridium Mixed-Metal Nitrido-Carbonyl Clusters. Synthesis, Characterization, Redox Properties, and Solid-State Structure of the Octahedral Clusters [Fe(5)RhN(CO)(15)](2)(-), [Fe(5)IrN(CO)(15)](2)(-), and [Fe(4)Rh(2)N(CO)(15)](-). Infrared and Nuclear Magnetic Resonance Spectroscopic Studies on the Interstitial Nitride.

PubMed

Della Pergola, Roberto; Cinquantini, Arnaldo; Diana, Eliano; Garlaschelli, Luigi; Laschi, Franco; Luzzini, Paola; Manassero, Mario; Repossi, Andrea; Sansoni, Mirella; Stanghellini, Pier Luigi; Zanello, Piero

1997-08-13

The cluster [Fe(5)RhN(CO)(15)](2)(-) was synthesized in 40% yield from [Fe(4)N(CO)(12)](-) and [Rh(CO)(4)](-) in refluxing tetrahydrofuran, whereas the analogous anion [Fe(5)IrN(CO)(15)](2)(-) was prepared in CH(3)CN at room temperature from [Fe(6)N(CO)(15)](3)(-) and [Ir(C(8)H(14))(2)Cl](2); the yields are higher than 60%. The monoanion [Fe(4)Rh(2)N(CO)(15)](-) was obtained in 70% yield from [Fe(5)RhN(CO)(15)](2)(-) and hydrated RhCl(3). The solid-state structures of the three anions were determined on their [PPh(4)](+) salts: the six metal atoms are arranged in octahedral cages and are coordinated to 3 edge-bridging and 12 terminal carbonyl ligands and to a &mgr;(6)-N ligand. The Rh and Ir atoms have less terminal COs than Fe, in order to equalize the excess electrons at the d(9) metal centers. The two rhodium atoms in [Fe(4)Rh(2)N(CO)(15)](-) are directly bound. The (15)N NMR spectra of the three compounds have been recorded; the signals of the nitride ligands were found at delta = 514 ppm for the dianions and 470 ppm for [Fe(4)Rh(2)N(CO)(15)](-); any group 9 atom shifts the resonance of nitrogen to higher fields. The coupling constants J((15)N-(103)Rh) are 8-9 Hz. The vibrational patterns of the metal cores have been interpreted on the basis of an idealized M(6) octahedral arrangement, subsequently modified by the perturbations given by different atomic masses and M-M stretching force constants. The motions of the nitrogen are related to the idealized symmetry of the cage; the M-N force constant values depend on the type of metal and on the charge of the anion. The dianions [Fe(5)MN(CO)(15)](2)(-) can be electrochemically oxidized at -20 degrees C to their short-lived monoanions, which can be characterized by EPR spectroscopy. In contrast, the cluster [Fe(4)Rh(2)N(CO)(15)](-) undergoes a single-step 2-electron reduction to the partially stable trianion [Fe(4)Rh(2)N(CO)(15)](3)(-), which was also characterized by EPR spectroscopy. The Fe-Rh nitride clusters are

Electron spin resonance and electron spin echo modulation of n-doxylstearic acid and N,N,N',N'-tetramethylbenzidine photoionization in sodium versus lithium dodecyl sulfate micellar solutions: effect of 15-crown-5 and 18-crown-6 ether addition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baglioni, P.; Rivara-Minten, E.; Kevan, L.

1988-08-11

Electron spin echo modulation and electron spin resonance spectra of photogenerated N,N,N',N'-tetramethylbenzidine (TMB) cation radical and n-doxylstearic acids (n-DSA) in frozen micellar solutions of sodium and lithium dodecyl sulfate containing 15-crown-5 and 18-crown-6 ethers in D/sub 2/O have been studied as a function of crown ether concentration. Modulation effects due to N-DSA with water deuteriums give direct evidence that both crown ethers are mainly located at the micellar interface and that this causes a decrease of the hydration of the micellar interface. Crown ether complexation constants for sodium and lithium micellar counterions are reported and show that 18-crown-6 > 15-crown-5more » for sodium counterion and 15-crown-5 > 18-crown-6 for lithium counterion. Modulation effects from TMB/sup +/ interaction with water deuteriums indicate that the TMB molecule moves toward the micelle interfacial region when sodium or lithium cations are complexed by crown ethers. The TMB/sup +/ yield upon TMB photoionization increases by about 10% with crown ether addition for SDS and LDS micellar systems, but it is greater if the absolute values for the LDS system are compared to those for the SDS micellar system. This behavior correlates with the strength of TMB/sup +/-water interactions and suggests that the main factor in the photoionization efficiency is the photocation-water interaction.« less

Resonance assignments for the substrate binding domain of Hsp70 chaperone Ssa1 from Saccharomyces cerevisiae.

PubMed

Hu, Wanhui; Wu, Huiwen; Zhang, Hong; Gong, Weibin; Perrett, Sarah

2015-10-01

Hsp70 chaperone proteins play crucial roles in the cell. Extensive structural and functional studies have been performed for bacterial and mammalian Hsp70s. Ssa1 from Saccharomyces cerevisiae is a member of the Hsp70 family. In vivo and biochemical studies on Ssa1 have revealed that it regulates prion propagation and the cell cycle. However, no structural data has been obtained for Ssa1 up to now. Here we report the almost complete (96 %) (1)H, (13)C, (15)N backbone and side chain NMR assignment of the 18.8 kDa Ssa1 substrate binding domain. The construct includes residues 382-554, which corresponds to the entire substrate binding domain and two following α-helices in homologous structures. The secondary structure predicted from the assigned chemical shifts is consistent with that of homologous Hsp70 substrate binding domains.

Fermi resonance in CO2: Mode assignment and quantum nuclear effects from first principles molecular dynamics

NASA Astrophysics Data System (ADS)

Basire, Marie; Mouhat, Félix; Fraux, Guillaume; Bordage, Amélie; Hazemann, Jean-Louis; Louvel, Marion; Spezia, Riccardo; Bonella, Sara; Vuilleumier, Rodolphe

2017-04-01

Vibrational spectroscopy is a fundamental tool to investigate local atomic arrangements and the effect of the environment, provided that the spectral features can be correctly assigned. This can be challenging in experiments and simulations when double peaks are present because they can have different origins. Fermi dyads are a common class of such doublets, stemming from the resonance of the fundamental excitation of a mode with the overtone of another. We present a new, efficient approach to unambiguously characterize Fermi resonances in density functional theory (DFT) based simulations of condensed phase systems. With it, the spectral features can be assigned and the two resonating modes identified. We also show how data from DFT simulations employing classical nuclear dynamics can be post-processed and combined with a perturbative quantum treatment at a finite temperature to include analytically thermal quantum nuclear effects. The inclusion of these effects is crucial to correct some of the qualitative failures of the Newtonian dynamics simulations at a low temperature such as, in particular, the behavior of the frequency splitting of the Fermi dyad. We show, by comparing with experimental data for the paradigmatic case of supercritical CO2, that these thermal quantum effects can be substantial even at ambient conditions and that our scheme provides an accurate and computationally convenient approach to account for them.

¹⁵N, ¹³C and ¹H resonance assignments and secondary structure determination of a variable heavy domain of a heavy chain antibody.

PubMed

Prosser, Christine E; Waters, Lorna C; Muskett, Frederick W; Veverka, Vaclav; Addis, Philip W; Griffin, Laura M; Baker, Terry S; Lawson, Alastair D G; Wernery, Ulrich; Kinne, Jorg; Henry, Alistair J; Taylor, Richard J; Carr, Mark D

2014-04-01

Heavy chain antibodies differ in structure to conventional antibodies lacking both the light chain and the first heavy chain constant domain (CH1). Characteristics of the antigen-binding variable heavy domain of the heavy chain antibody (VHH) including the smaller size, high solubility and stability make them an attractive alternative to more traditional antibody fragments for detailed NMR-based structural analysis. Here we report essentially complete backbone and side chain (15)N, (13)C and (1)H assignments for a free VHH. Analysis of the backbone chemical shift data obtained indicates that the VHH is comprised predominantly of β-sheets corresponding to nearly 60% of the protein backbone.

Kinetic 15N-isotope effects on algal growth

NASA Astrophysics Data System (ADS)

Andriukonis, Eivydas; Gorokhova, Elena

2017-03-01

Stable isotope labeling is a standard technique for tracing material transfer in molecular, ecological and biogeochemical studies. The main assumption in this approach is that the enrichment with a heavy isotope has no effect on the organism metabolism and growth, which is not consistent with current theoretical and empirical knowledge on kinetic isotope effects. Here, we demonstrate profound changes in growth dynamics of the green alga Raphidocelis subcapitata grown in 15N-enriched media. With increasing 15N concentration (0.37 to 50 at%), the lag phase increased, whereas maximal growth rate and total yield decreased; moreover, there was a negative relationship between the growth and the lag phase across the treatments. The latter suggests that a trade-off between growth rate and the ability to adapt to the high 15N environment may exist. Remarkably, the lag-phase response at 3.5 at% 15N was the shortest and deviated from the overall trend, thus providing partial support to the recently proposed Isotopic Resonance hypothesis, which predicts that certain isotopic composition is particularly favorable for living organisms. These findings confirm the occurrence of KIE in isotopically enriched algae and underline the importance of considering these effects when using stable isotope labeling in field and experimental studies.

15N Hyperpolarization by Reversible Exchange Using SABRE-SHEATH

PubMed Central

2016-01-01

NMR signal amplification by reversible exchange (SABRE) is a NMR hyperpolarization technique that enables nuclear spin polarization enhancement of molecules via concurrent chemical exchange of a target substrate and parahydrogen (the source of spin order) on an iridium catalyst. Recently, we demonstrated that conducting SABRE in microtesla fields provided by a magnetic shield enables up to 10% 15N-polarization (Theis, T.; et al. J. Am. Chem. Soc.2015, 137, 1404). Hyperpolarization on 15N (and heteronuclei in general) may be advantageous because of the long-lived nature of the hyperpolarization on 15N relative to the short-lived hyperpolarization of protons conventionally hyperpolarized by SABRE, in addition to wider chemical shift dispersion and absence of background signal. Here we show that these unprecedented polarization levels enable 15N magnetic resonance imaging. We also present a theoretical model for the hyperpolarization transfer to heteronuclei, and detail key parameters that should be optimized for efficient 15N-hyperpolarization. The effects of parahydrogen pressure, flow rate, sample temperature, catalyst-to-substrate ratio, relaxation time (T1), and reversible oxygen quenching are studied on a test system of 15N-pyridine in methanol-d4. Moreover, we demonstrate the first proof-of-principle 13C-hyperpolarization using this method. This simple hyperpolarization scheme only requires access to parahydrogen and a magnetic shield, and it provides large enough signal gains to enable one of the first 15N images (2 × 2 mm2 resolution). Importantly, this method enables hyperpolarization of molecular sites with NMR T1 relaxation times suitable for biomedical imaging and spectroscopy. PMID:25960823

15N Hyperpolarization by Reversible Exchange Using SABRE-SHEATH.

PubMed

Truong, Milton L; Theis, Thomas; Coffey, Aaron M; Shchepin, Roman V; Waddell, Kevin W; Shi, Fan; Goodson, Boyd M; Warren, Warren S; Chekmenev, Eduard Y

2015-04-23

NMR signal amplification by reversible exchange (SABRE) is a NMR hyperpolarization technique that enables nuclear spin polarization enhancement of molecules via concurrent chemical exchange of a target substrate and parahydrogen (the source of spin order) on an iridium catalyst. Recently, we demonstrated that conducting SABRE in microtesla fields provided by a magnetic shield enables up to 10% 15 N-polarization (Theis, T.; et al. J. Am. Chem. Soc. 2015 , 137 , 1404). Hyperpolarization on 15 N (and heteronuclei in general) may be advantageous because of the long-lived nature of the hyperpolarization on 15 N relative to the short-lived hyperpolarization of protons conventionally hyperpolarized by SABRE, in addition to wider chemical shift dispersion and absence of background signal. Here we show that these unprecedented polarization levels enable 15 N magnetic resonance imaging. We also present a theoretical model for the hyperpolarization transfer to heteronuclei, and detail key parameters that should be optimized for efficient 15 N-hyperpolarization. The effects of parahydrogen pressure, flow rate, sample temperature, catalyst-to-substrate ratio, relaxation time ( T 1 ), and reversible oxygen quenching are studied on a test system of 15 N-pyridine in methanol- d 4 . Moreover, we demonstrate the first proof-of-principle 13 C-hyperpolarization using this method. This simple hyperpolarization scheme only requires access to parahydrogen and a magnetic shield, and it provides large enough signal gains to enable one of the first 15 N images (2 × 2 mm 2 resolution). Importantly, this method enables hyperpolarization of molecular sites with NMR T 1 relaxation times suitable for biomedical imaging and spectroscopy.

New assignment of 14N NQR spectral lines for tetrazoles derivatives

NASA Astrophysics Data System (ADS)

Mamadazizov, Sultonazar; Shelyapina, Marina G.; Kupriyanova, Galina S.; Mozzhukhin, George V.

2018-04-01

In recent years, considerable interest has been shown in the study of tetrazole derivatives, which attract attention as highly nitrogenous compounds for use as an isosteric substitutes for various functional groups that leads to creation of novel biologically active substances. NQR techniques, being sensitive to the local environment of 14N nuclei, provide great opportunities to study these new substances. To make investigation of complex compounds containing tetrazoles derivatives easier and more reliable a correctly assigned 14N NQR spectra of tetrazoles are required. Here we report on the results of our DFT B3LYP calculations of 14N NQR spectral parameters (quadrupole coupling constant Qcc and the asymmetry parameter of the electric field gradient η) for tetrazole, 5-aminotetrazole and 5-aminotetrazole monohydrate. It has been found that the commonly accepted assignment of the 14N NQR spectral lines for these molecules is incorrect. A new assignment for these molecules is proposed.

Zigzag spin structure in layered honeycomb L i3N i2Sb O6 : A combined diffraction and antiferromagnetic resonance study

NASA Astrophysics Data System (ADS)

Kurbakov, A. I.; Korshunov, A. N.; Podchezertsev, S. Yu.; Malyshev, A. L.; Evstigneeva, M. A.; Damay, F.; Park, J.; Koo, C.; Klingeler, R.; Zvereva, E. A.; Nalbandyan, V. B.

2017-07-01

The magnetic structure of L i3N i2Sb O6 has been determined by low-temperature neutron diffraction, and the crystal structure has been refined by a combination of synchrotron and neutron powder diffraction. The monoclinic (C 2 /m ) symmetry, assigned previously to this pseudohexagonal layered structure, has been unambiguously proven by peak splitting in the synchrotron diffraction pattern. The structure is based on essentially hexagonal honeycomb-ordered N i2Sb O6 layers alternating with L i3 layers, all cations and anions being in an octahedral environment. The compound orders antiferromagnetically below TN=15 K , with the magnetic supercell being a 2 a ×2 b multiple of the crystal cell. The magnetic structure within the honeycomb layer consists of zigzag ferromagnetic spin chains coupled antiferromagnetically. The ordered magnetic moment amounts to 1.62 (2 ) μB/Ni , which is slightly lower than the full theoretical value. Upon cooling below TN, the spins tilt from the c axis, with a maximum tilting angle of 15 .6∘ at T =1.5 K . Our data imply non-negligible ferromagnetic interactions between the honeycomb layers. The observed antiferromagnetic resonance modes are in agreement with the two-sublattice model derived from the neutron data. Orthorhombic anisotropy shows up in zero-field splitting of Δ =198 ±4 and 218 ±4 GHz . Above TN, the electron spin resonance data imply short-range antiferromagnetic order up to about 80 K.

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

PubMed Central

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

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 resonances and large differences in chemical shifts (Δδ >90 ppm) between their free base and protonated forms. These favorable features make these agents highly suitable candidates for the detection of small changes in tissue pH near physiological values. PMID:25774436

High-Precision Measurements of 15N15N, 14N15N, and 14N2 in N2 and Potential Applications to Oceanic Nitrogen Cycle Research

NASA Astrophysics Data System (ADS)

Li, S.; Yeung, L.; Young, E. D.; Ostrom, N. E.; Haslun, J. A.

2016-02-01

The balance of nitrogen fixation and nitrogen loss in the oceans is uncertain. For example, anaerobic ammonia oxidation could account for 50% or more of marine N2 production, although its global importance is still poorly known. Isotopic ratios in fixed nitrogen species (e.g., δ15N and δ18O values of NO2- and NO3-) are widely used to trace preservation and removal of N-bearing compounds and/or isotopic variations of their different sources. However, these approaches in general probe only one side of the nitrogen mass balance—the "fixed" nitrogen reservoir—so they offer few constraints on the ultimate loss of nitrogen from that pool as N2. The rare isotopologue ratio 15N15N/14N2 in N2may provide information about those nitrogen-loss processes directly. We will report the first measurements of Δ30 (the abundance of 15N15N relative to that predicted by chance alone), made on a unique high-resolution mass spectrometer (the Nu Instruments Panorama), and we will discuss the potential utility of Δ30 as an independent tracer of the nitrogen cycle. The parameter Δ30 is insensitive to the bulk 15N/14N isotopic ratio of the reservoir; instead, it reflects isotopic ordering in N2, which is altered when N-N bonds are made or broken. Our preliminary measurements of N2 from denitrifying soils and pure cultures of denitrifiers indicate large kinetic isotopic effects during N-N bond formation that favor 15N15N production during denitrification. We also observed a nonstochastic excess of 15N15N in tropospheric N2 [Δ30 = +19.05 ± 0.12‰ (1σ)]. This excess likely comes from fixed-nitrogen loss processes in the biosphere. Variations in Δ30 of N2 from pure culture experiments (+16.96 to +18.95‰) probably reflect the different isotopic signatures of the enzymes that catalyze denitrification. So, enzyme-specific Δ30 values of dissolved N2 should provide information about the importance of different biochemical pathways of fixed-nitrogen loss (e.g., denitrification vs

15 CFR 806.18 - OMB control numbers assigned to the Paperwork Reduction Act.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 15 Commerce and Foreign Trade 3 2010-01-01 2010-01-01 false OMB control numbers assigned to the Paperwork Reduction Act. 806.18 Section 806.18 Commerce and Foreign Trade Regulations Relating to Commerce and Foreign Trade (Continued) BUREAU OF ECONOMIC ANALYSIS, DEPARTMENT OF COMMERCE DIRECT INVESTMENT...

Amino Acid Selective 13C Labeling and 13C Scrambling Profile Analysis of Protein α and Side-Chain Carbons in Escherichia coli Utilized for Protein Nuclear Magnetic Resonance.

PubMed

Sugiki, Toshihiko; Furuita, Kyoko; Fujiwara, Toshimichi; Kojima, Chojiro

2018-06-20

Amino acid selective isotope labeling is an important nuclear magnetic resonance technique, especially for larger proteins, providing strong bases for the unambiguous resonance assignments and information concerning the structure, dynamics, and intermolecular interactions. Amino acid selective 15 N labeling suffers from isotope dilution caused by metabolic interconversion of the amino acids, resulting in isotope scrambling within the target protein. Carbonyl 13 C atoms experience less isotope scrambling than the main-chain 15 N atoms do. However, little is known about the side-chain 13 C atoms. Here, the 13 C scrambling profiles of the Cα and side-chain carbons were investigated for 15 N scrambling-prone amino acids, such as Leu, Ile, Tyr, Phe, Thr, Val, and Ala. The level of isotope scrambling was substantially lower in 13 Cα and 13 C side-chain labeling than in 15 N labeling. We utilized this reduced scrambling-prone character of 13 C as a simple and efficient method for amino acid selective 13 C labeling using an Escherichia coli cold-shock expression system and high-cell density fermentation. Using this method, the 13 C labeling efficiency was >80% for Leu and Ile, ∼60% for Tyr and Phe, ∼50% for Thr, ∼40% for Val, and 30-40% for Ala. 1 H- 15 N heteronuclear single-quantum coherence signals of the 15 N scrambling-prone amino acid were also easily filtered using 15 N-{ 13 Cα} spin-echo difference experiments. Our method could be applied to the assignment of the 55 kDa protein.

Preparation of 13C/15N-labeled oligomers using the polymerase chain reaction

DOEpatents

Chen, Xian; Gupta, Goutam; Bradbury, E. Morton

2001-01-01

Preparation of .sup.13 C/.sup.15 N-labeled DNA oligomers using the polymerase chain reaction (PCR). A PCR based method for uniform (.sup.13 C/.sup.15 N)-labeling of DNA duplexes is described. Multiple copies of a blunt-ended duplex are cloned into a plasmid, each copy containing the sequence of interest and restriction Hinc II sequences at both the 5' and 3' ends. PCR using bi-directional primers and uniformly .sup.13 C/.sup.15 N-labeled dNTP precursors generates labeled DNA duplexes containing multiple copies of the sequence of interest. Twenty-four cycles of PCR, followed by restriction and purification, gave the uniformly .sup.13 C/.sup.15 N-labeled duplex sequence with a 30% yield. Such labeled duplexes find significant applications in multinuclear magnetic resonance spectroscopy.

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.

PubMed

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. (c) 2007 John Wiley & Sons, Ltd.

NMR of enzymatically synthesized uniformly 13C15N-labeled DNA oligonucleotides.

PubMed Central

Zimmer, D P; Crothers, D M

1995-01-01

A procedure for the enzymatic synthesis of uniformly 13C15N-labeled DNA oligonucleotides in milligram quantities for NMR studies is described. Deoxynucleotides obtained from microorganisms grown on 13C and 15N nutrient sources are enzymatically phosphorylated to dNTPs, and the dNTPs are incorporated into oligonucleotides using a 3'-5' exonuclease-deficient mutant of Klenow fragment of DNA polymerase I and an oligonucleotide template primer designed for efficient separation of labeled product DNA from unlabeled template. The labeling strategy has been used to uniformly label one or the other oligonucleotide strand in the DNA duplex dGGCAAAACGG.dCCGTTTTGCC in order to facilitate assignment and structure determination by NMR. Application of 15N and 13C heteronuclear NMR experiments to isotopically labeled DNA is presented. Images Fig. 2 Fig. 3 Fig. 4 PMID:7724521

Does fertilizer (N15P15K15) amendment enhance phytoremediation of petroleum-polluted aquatic ecosystem in the presence of water hyacinth (Eichhornia crassipes [Mart.] Solms)?

PubMed

Ndimele, Prince Emeka; Jenyo-Oni, Adetola; Chukwuka, Kanayo S; Ndimele, Chinatu Charity; Ayodele, Ibukunoluwa Augustine

2015-01-01

This study investigated the effects of inorganic fertilizer (N15P15K15) amendments on crude oil uptake by water hyacinth. Experimental units (water hyacinth grown in fresh water) were spiked with 0, 20, 40 and 60 mg/L crude oil. After 24 h, they were randomly assigned fertilizer (N15P15K15) at three different concentrations; 0, 6 and 10 mg/L. Crude oil degradation and absorption were determined by measuring total petroleum hydrocarbon (TPH) in the water column and water hyacinth, respectively. The measurements were taken monthly for six months (February-August 2010). The results showed that TPH concentration in the water column in the treatment amended at 6 mg/L (0.30 ± 0.01 mg/L) was significantly lower (p < .05) than the treatment amended at 10 mg/L (0.76 ± 0.15 mg/L) but was similar to the control (0.33 ± 0.03 mg/L). The water hyacinth in the control (phytoremediation) absorbed significantly higher (p < .05) TPH than the fertilizer-amended treatments. The first-order kinetic model gave a better description of the degradation of petroleum hydrocarbons. The study showed that phytoremediation of crude oil by water hyacinth and biostimulation with fertilizer (N15P15K15) is possible.

Nitrite fixation by humic substances: Nitrogen-15 nuclear magnetic resonance evidence for potential intermediates in chemodenitrification

USGS Publications Warehouse

Thorn, K.A.; Mikita, M.A.

2000-01-01

Studies have suggested that NO2/-, produced during nitrification and denitrification, can become incorporated into soil organic matter and, in one of the processes associated with chemodenitrification, react with organic matter to form trace N gases, including N2O. To gain an understanding of the nitrosation chemistry on a molecular level, soil and aquatic humic substances were reacted with 15N-labeled NaNO2, and analyzed by liquid phase 15N and 13C nuclear magnetic resonance (NMR). The International Humic Substances Society (IHSS) Pahokee peat and peat humic acid were also reacted with Na15NO2 and analyzed by solid-state 15N NMR. In Suwannee River, Armadale, and Laurentian fulvic acids, phenolic rings and activated methylene groups underwent nitrosation to form nitrosophenols (quinone monoximes) and ketoximes, respectively. The oximes underwent Beckmann rearrangements to 2??amides, and Beckmann fragmentations to nitriles. The nitriles in turn underwent hydrolysis to 1??amides. Peaks tentatively identified as imine, indophenol, or azoxybenzene nitrogens were clearly present in spectra of samples nitrosated at pH 6 but diminished at pH 3. The 15N NMR spectrum of the peat humic acid exhibited peaks corresponding with N-nitroso groups in addition to nitrosophenols, ketoximes, and secondary Beckmann reaction products. Formation of N-nitroso groups was more significant in the whole peat compared with the peat humic acid. Carbon-13 NMR analyses also indicated the occurrence of nitrosative demethoxylation in peat and soil humic acids. Reaction of 15N-NH3 fixated fulvic acid with unlabeled NO2/- resulted in nitrosative deamination of aminohydroquinone N, suggesting a previously unrecognized pathway for production of N2 gas in soils fertilized with NH3.Studies have suggested that NO2-, produced during nitrification and denitrification, can become incorporated into soil organic matter and, in one of the processes associated with chemodenitrification, react with organic

Design of a 15N Molecular Unit to Achieve Long Retention of Hyperpolarized Spin State

NASA Astrophysics Data System (ADS)

Nonaka, Hiroshi; Hirano, Masashi; Imakura, Yuki; Takakusagi, Yoichi; Ichikawa, Kazuhiro; Sando, Shinsuke

2017-01-01

Nuclear hyperpolarization is a phenomenon that can be used to improve the sensitivity of magnetic resonance molecular sensors. However, such sensors typically suffer from short hyperpolarization lifetime. Herein we report that [15N, D14]trimethylphenylammonium (TMPA) has a remarkably long spin-lattice relaxation time (1128 s, 14.1 T, 30 °C, D2O) on its 15N nuclei and achieves a long retention of the hyperpolarized state. [15N, D14]TMPA-based hyperpolarized sensor for carboxylesterase allowed the highly sensitive analysis of enzymatic reaction by 15N NMR for over 40 min in phophate-buffered saline (H2O, pH 7.4, 37 °C).

High-resolution Fourier-transform extreme ultraviolet photoabsorption spectroscopy of 14N15N

NASA Astrophysics Data System (ADS)

Heays, A. N.; Dickenson, G. D.; Salumbides, E. J.; de Oliveira, N.; Joyeux, D.; Nahon, L.; Lewis, B. R.; Ubachs, W.

2011-12-01

The first comprehensive high-resolution photoabsorption spectrum of 14N15N has been recorded using the Fourier-transform spectrometer attached to the Desirs beamline at the Soleil synchrotron. Observations are made in the extreme ultraviolet and span 100 000-109 000 cm-1 (100-91.7 nm). The observed absorption lines have been assigned to 25 bands and reduced to a set of transition energies, f values, and linewidths. This analysis has verified the predictions of a theoretical model of N2 that simulates its photoabsorption and photodissociation cross section by solution of an isotopomer independent formulation of the coupled-channel Schrödinger equation. The mass dependence of predissociation linewidths and oscillator strengths is clearly evident and many local perturbations of transition energies, strengths, and widths within individual rotational series have been observed.

Structure of indazole N1-oxide derivatives studied by X-ray, theoretical methods, 1H, 13C, 15N NMR and EI/MS

NASA Astrophysics Data System (ADS)

Gerpe, Alejandra; Piro, Oscar E.; Cerecetto, Hugo; González, Mercedes

2007-12-01

A series of indazole N1-oxide derivatives has been spectroscopically studied in solution using 1H, 13C, and 15N NMR based on pulsed field gradient selected PFG 1H sbnd X (X = 13C and 15N) gHMQC and gHMBC experiments. Some indazoles were prepared using a new methodology to compare its spectral and structural data with the indazole N1-oxide parent compounds. The 13C resonances of the indazole N1-oxide carbon 3 and 7a demonstrate the N-oxide push-electron capability. The 15N resonances of the indazole N-oxide, nitrogen 1, are near to 30 ppm more shielded than the corresponding values in the indazole heterocycle (deoxygenated form). Moreover, the structures of one indazole and one indazole N-oxide were unambiguously confirmed by X-ray crystallography. The solid state structures were contrasted with the theoretical ones obtained in vacuo at different calculus level. The aromaticity of the derivatives was studied analyzing the H sbnd H coupling constants of indazole's aromatic hydrogens and measuring C sbnd C distances in the solid state. The fragmentation that takes place in EI/MS was gathered for all the indazole N-oxide derivatives and the general fragmentation pattern analyzed.

Reactive Resonances in N+N2 Exchange Reaction

NASA Technical Reports Server (NTRS)

Wang, Dunyou; Huo, Winifred M.; Dateo, Christopher E.; Schwenke, David W.; Stallcop, James R.

2003-01-01

Rich reactive resonances are found in a 3D quantum dynamics study of the N + N2 exchange reaction using a recently developed ab initio potential energy surface. This surface is characterized by a feature in the interaction region called Lake Eyring , that is, two symmetric transition states with a shallow minimum between them. An L2 analysis of the quasibound states associated with the shallow minimum confirms that the quasibound states associated with oscillations in all three degrees of freedom in Lake Eyring are responsible for the reactive resonances in the state-to-state reaction probabilities. The quasibound states, mostly the bending motions, give rise to strong reasonance peaks, whereas other motions contribute to the bumps and shoulders in the resonance structure. The initial state reaction probability further proves that the bending motions are the dominating factors of the reaction probability and have longer life times than the stretching motions. This is the first observation of reactive resonances from a "Lake Eyring" feature in a potential energy surface.

On the extraction of P 11 resonances from πN data

DOE PAGES

Hiroyuki Kamano; Nakamura, Satoshi X.; Lee, Tsung -Shung; ...

2010-06-22

With the accuracy of the available P 11 amplitudes of πΔ scattering, we show that two resonance poles near the pi Delta threshold, obtained in several analyses, are stable against large variations of parameters within a dynamical coupled-channels analysis. The number of poles in the 1.5 GeV < W < 2 GeV region could be more than one, depending on how the structure of the single-energy solution of SAID is fitted. Lastly, our results indicate the need of more accurate πN scattering data in the W > 1.6 GeV region for high precision resonance extractions.

Modeling and optimization of a double-well double-barrier GaN/AlGaN/GaN/AlGaN resonant tunneling diode

NASA Astrophysics Data System (ADS)

Liu, Yang; Gao, Bo; Gong, Min; Shi, Ruiying

2017-06-01

The influence of a GaN layer as a sub-quantum well for an AlGaN/GaN/AlGaN double barrier resonant tunneling diode (RTD) on device performance has been investigated by means of numerical simulation. The introduction of the GaN layer as the sub-quantum well turns the dominant transport mechanism of RTD from the 3D-2D model to the 2D-2D model and increases the energy difference between tunneling energy levels. It can also lower the effective height of the emitter barrier. Consequently, the peak current and peak-to-valley current difference of RTD have been increased. The optimal GaN sub-quantum well parameters are found through analyzing the electrical performance, energy band, and transmission coefficient of RTD with different widths and depths of the GaN sub-quantum well. The most pronounced electrical parameters, a peak current density of 5800 KA/cm2, a peak-to-valley current difference of 1.466 A, and a peak-to-valley current ratio of 6.35, could be achieved by designing RTD with the active region structure of GaN/Al0.2Ga0.8 N/GaN/Al0.2Ga0.8 N (3 nm/1.5 nm/1.5 nm/1.5 nm).

Clinical Benefit of 3 Tesla Magnetic Resonance Imaging Rescanning in Patients With Focal Epilepsy and Negative 1.5 Tesla Magnetic Resonance Imaging.

PubMed

Ladino, Lady D; Balaguera, Pedro; Rascovsky, Simon; Delgado, Jorge; Llano, Juan; Hernández-Ronquillo, Lizbeth; Gómez-Arias, Bety; Téllez-Zenteno, José F

2016-01-01

Magnetic resonance imaging is an essential tool in the pre-surgical evaluation of patients with drug-resistant epilepsy. Our aim was to assess the value of re-imaging patients with focal drug-resistant epilepsy. Thirty patients with negative or non-conclusive 1.5 Tesla magnetic resonance imaging were rescanned with 1.5T and 3T. All of them had previous 1.5 scans with no seizure protocol in a non-specialized center. Two neuroradiologists who were blinded to prior imaging results randomly reviewed the magnetic resonance images. Kappa score was used to assess the reliability. Mean age of patients was 30 (SD ± 11) years. The intra-observer agreement for the first radiologist was 0.74 for 1.5T and 0.71 for 3T. In the second radiologist it was 0.82 and 0.66, respectively. Three lesions (10%) were identified by general radiologists in non-specialized centers using a 1.5T standard protocol. In our center a consensus between two neuroradiologists using epilepsy protocol identified seven lesions (23%) using 1.5T and 10 (33%) using 3T (p < 0.01). In 28% of patients this additional information resulted in a change in clinical management. 3T magnetic resonance imaging rescanning improves the diagnostic yield in patients with focal epilepsy and previous negative 1.5T magnetic resonance imaging. Use of 3T magnetic resonance imaging, epilepsy protocols, and interpretation by experienced neuroradiologists is highly recommended.

Search for unbound 15Be states in the 3 n +12Be channel

NASA Astrophysics Data System (ADS)

Kuchera, A. N.; Spyrou, A.; Smith, J. K.; Baumann, T.; Christian, G.; DeYoung, P. A.; Finck, J. E.; Frank, N.; Jones, M. D.; Kohley, Z.; Mosby, S.; Peters, W. A.; Thoennessen, M.

2015-01-01

Background: 15Be is expected to have low-lying 3 /2+ and 5 /2+ states. A first search did not find the 3 /2+ [A. Spyrou et al., Phys. Rev. C 84, 044309 (2011), 10.1103/PhysRevC.84.044309]; however, a resonance in 15Be was populated in a second attempt and determined to be unbound with respect to 14Be by 1.8(1) MeV with a tentative spin-parity assignment of 5 /2+ [J. Snyder et al., Phys. Rev. C 88, 031303(R) (2013), 10.1103/PhysRevC.88.031303]. Purpose: Search for the predicted 15Be 3 /2+ state in the three-neutron decay channel. Method: A two-proton removal reaction from a 55 MeV/u 17C beam was used to populate neutron-unbound states in 15Be. The two-, three-, and four-body decay energies of the 12Be + neutron(s) detected in coincidence were reconstructed using invariant mass spectroscopy. Monte Carlo simulations were performed to extract the resonance and decay properties from the observed spectra. Results: The low-energy regions of the decay energy spectra can be described with the first excited unbound state of 14Be (Ex=1.54 MeV, Er=0.28 MeV). Including a state in 15Be that decays through the first excited 14Be state slightly improves the fit at higher energies though the cross section is small. Conclusions: A 15Be component is not needed to describe the data. If the 3 /2+ state in 15Be is populated, the decay by three-neutron emission through 14Be is weak, ≤11 % up to 4 MeV. In the best fit, 15Be is unbound with respect to 12Be by 1.4 MeV (unbound with respect to 14Be by 2.66 MeV) with a strength of 7 % .

Coulomb and nuclear excitations of narrow resonances in 17Ne

DOE PAGES

Marganiec, J.; Wamers, F.; Aksouh, F.; ...

2016-05-25

New experimental data for dissociation of relativistic 17Ne projectiles incident on targets of lead, carbon, and polyethylene targets at GSI are presented. Special attention is paid to the excitation and decay of narrow resonant states in 17Ne. Distributions of internal energy in the 15O+p +p three-body system have been determined together with angular and partial-energy correlations between the decay products in different energy regions. The analysis was done using existing experimental data on 17Ne and its mirror nucleus 17N. The isobaric multiplet mass equation is used for assignment of observed resonances and their spins and parities. A combination of datamore » from the heavy and light targets yielded cross sections and transition probabilities for the Coulomb excitations of the narrow resonant states. Finally, the resulting transition probabilities provide information relevant for a better understanding of the 17Ne structure.« less

Application of INEPT nitrogen-15 and silicon-29 nuclear magnetic resonance spectrometry to derivatized fulvic acids

USGS Publications Warehouse

Thorn, K.A.; Folan, D.W.; Arterburn, J.B.; Mikita, M.A.; MacCarthy, P.

1989-01-01

Use of the INEPT experiment has been examined in two derivatization studies of the Suwannee River fulvic acid. In the first study, the fulvic acid was derivatized with 15N enriched hydroxylamine. The quantitative 15N NMR spectrum, acquired with a 45° pulse angle, 2.0 second pulse delay and inverse gated decoupling, showed that oximes (390-340 ppm) were the major derivatives, followed by nitriles (270-240 ppm), hydroxamic acids (170-160 ppm), secondary amides (150-115 ppm), and lactams (115-90 ppm). The INEPT 15N NMR spectrum was acquired using refocussing delays and polarization transfer times optimized for signal enhancement of singly protonated nitrogens. INEPT greatly enhanced the amide and lactam resonances, and showed that resonances downfield of 180 ppm in the quantitative spectrum represented nonprotonated nitrogens. In the second study, the fulvic acid was first methylated with diazomethane and then silylated with hexamethyldisilazane. The 29Si NMR spectra exhibited two major peaks, from approximately 33 to 22 ppm, representing silyl esters of carboxylic acids, and from 22 to 13 ppm, representing silyl ethers of alcohols and phenols. The INEPT 29Si NMR spectrum was virtually identical to the quantitative 29Si spectrum, acquired with a 90° pulse angle, 5.0 second pulse delay, inverse gated decoupling, and relaxation reagent. INEPT therefore can be used for quantitative analysis of trimethylsilyl derivatives of the fulvic acid, saving spectrometer time and eliminating the need for relaxation reagents.

sup 1 H assignments and secondary structure determination of the soybean trypsin/chymotrypsin Bowman-Birk inhibitor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Werner, M.H.; Wemmer, D.E.

1991-04-09

The {sup 1}H resonance assignments and secondary structure of the trypsin/chymotrypsin Bowman-Birk inhibitor from soybeans were determined by nuclear magnetic resonance spectroscopy (NMR) at 600 MHz in an 18% acetonitrile-d{sub 3}/aqueous cosolvent. Resonances from 69 to 71 amino acids were assigned sequence specifically. Residues Q11-T15 form an antiparallel {beta}-sheet with residues Q21-S25 in the tryptic inhibitory domain and an analogous region of antiparallel sheet forms between residues S38-A42 and Q48-V52 in the chymotryptic inhibitory domain. The inhibitory sites of each fragment (K16-S17 for trypsin, L43-S44 for chymotrypsin) are each part of a type VI like turn at one end ofmore » their respective region of the antiparallel {beta}-sheet. These structural elements are compared to those found in other Bowman-Birk inhibitors.« less

Asymmetric quantum-well structures for AlGaN/GaN/AlGaN resonant tunneling diodes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Lin'an, E-mail: layang@xidian.edu.cn; Li, Yue; Wang, Ying

Asymmetric quantum-well (QW) structures including the asymmetric potential-barrier and the asymmetric potential-well are proposed for AlGaN/GaN/AlGaN resonant tunneling diodes (RTDs). Theoretical investigation gives that an appropriate decrease in Al composition and thickness for emitter barrier as well as an appropriate increase of both for collector barrier can evidently improve the negative-differential-resistance characteristic of RTD. Numerical simulation shows that RTD with a 1.5-nm-thick GaN well sandwiched by a 1.3-nm-thick Al{sub 0.15}Ga{sub 0.85}N emitter barrier and a 1.7-nm-thick Al{sub 0.25}Ga{sub 0.75}N collector barrier can yield the I-V characteristic having the peak current (Ip) and the peak-to-valley current ratio (PVCR) of 0.39 A andmore » 3.6, respectively, about double that of RTD with a 1.5-nm-thick Al{sub 0.2}Ga{sub 0.8}N for both barriers. It is also found that an introduction of InGaN sub-QW into the diode can change the tunneling mode and achieve higher transmission coefficient of electron. The simulation demonstrates that RTD with a 2.8-nm-thick In{sub 0.03}Ga{sub 0.97}N sub-well in front of a 2.0-nm-thick GaN main-well can exhibit the I-V characteristic having Ip and PVCR of 0.07 A and 11.6, about 7 times and double the value of RTD without sub-QW, respectively. The purpose of improving the structure of GaN-based QW is to solve apparent contradiction between the device structure and the device manufacturability of new generation RTDs for sub-millimeter and terahertz applications.« less

Automatic Assignment of Methyl-NMR Spectra of Supramolecular Machines Using Graph Theory.

PubMed

Pritišanac, Iva; Degiacomi, Matteo T; Alderson, T Reid; Carneiro, Marta G; Ab, Eiso; Siegal, Gregg; Baldwin, Andrew J

2017-07-19

Methyl groups are powerful probes for the analysis of structure, dynamics and function of supramolecular assemblies, using both solution- and solid-state NMR. Widespread application of the methodology has been limited due to the challenges associated with assigning spectral resonances to specific locations within a biomolecule. Here, we present Methyl Assignment by Graph Matching (MAGMA), for the automatic assignment of methyl resonances. A graph matching protocol examines all possibilities for each resonance in order to determine an exact assignment that includes a complete description of any ambiguity. MAGMA gives 100% accuracy in confident assignments when tested against both synthetic data, and 9 cross-validated examples using both solution- and solid-state NMR data. We show that this remarkable accuracy enables a user to distinguish between alternative protein structures. In a drug discovery application on HSP90, we show the method can rapidly and efficiently distinguish between possible ligand binding modes. By providing an exact and robust solution to methyl resonance assignment, MAGMA can facilitate significantly accelerated studies of supramolecular machines using methyl-based NMR spectroscopy.

Deuterium isotope effects on 13C and 15N chemical shifts of intramolecularly hydrogen-bonded enaminocarbonyl derivatives of Meldrum’s and Tetronic acid

NASA Astrophysics Data System (ADS)

Ullah, Saif; Zhang, Wei; Hansen, Poul Erik

2010-07-01

Secondary deuterium isotope effects on 13C and 15N nuclear shieldings in a series of cyclic enamino-diesters and enamino-esters and acyclic enaminones and enamino-esters have been examined and analysed using NMR and DFT (B3LYP/6-31G(d,p)) methods. One-dimensional and two-dimensional NMR spectra of enaminocarbonyl and their deuterated analogues were recorded in CDCl 3 and CD 2Cl 2 at variable temperatures and assigned. 1JNH coupling constants for the derivatives of Meldrum's and tetronic acids reveal that they exist at the NH-form. It was demonstrated that deuterium isotope effects, for the hydrogen bonded compounds, due to the deuterium substitution at the nitrogen nucleus lead to large one-bond isotope effects at nitrogen, 1Δ 15N(D), and two-bond isotope effects on carbon nuclei, 2ΔC(ND), respectively. A linear correlations exist between 2ΔC(ND) and 1Δ 15N(D) whereas the correlation with δNH is divided into two. A good agreement between the experimentally observed 2ΔC(ND) and calculated dσ 13C/dR NH was obtained. A very good correlation between calculated NH bond lengths and observed NH chemical shifts is found. The observed isotope effects are shown to depend strongly on Resonance Assisted Hydrogen bonding.

Deciphering the fluorescence resonance energy transfer from denatured transport protein to anthracene 1,5 disulphonate in reverse micellar environment

NASA Astrophysics Data System (ADS)

Singharoy, Dipti; Bhattacharya, Subhash Chandra

2017-12-01

Constrained environmental effect inside AOT reverse micellar media has been employed in this work to collect the information about energy transfer efficacy between sodium salt of anthracene 1,5 disulphonate (1,5-AS) with model transport proteins, bovine serum albumin (BSA), and human serum albumin (HSA). Steady state, time-resolved fluorescence and circular dichroism techniques have been used for this purpose and corresponding Fӧrster-type resonance energy transfer (FRET) from tryptophan residues to 1,5-AS indicates that 1,5-AS binds in the vicinity of the tryptophan residue (BSA and HSA) with equal strength. Indication of protein damage from fluorescence data and its confirmation has been measured from CD measurement. Molecular modeling study hereby plays a crucial role to predict the minimum energy docked conformation of the probe inside the protein environment. From the docked conformation the distance between 1,5-AS and tryptophan moiety of BSA/HSA has successfully explained the FRET possibility between them. A comparative modeling study between BSA and HSA with 1,5-AS assigning their binding site within specific amino acids plays a crucial role in support of the FRET study.

NMR backbone resonance assignments of the prodomain variants of BDNF in the urea denatured state.

PubMed

Wang, Jing; Bains, Henrietta; Anastasia, Agustin; Bracken, Clay

2018-04-01

Brain derived neurotrophic factor (BDNF) is a member of the neurotrophin family of proteins which plays a central role in neuronal survival, growth, plasticity and memory. A single Val66Met variant has been identified in the prodomain of human BDNF that is associated with anxiety, depression and memory disorders. The structural differences within the full-length prodomain Val66 and Met66 isoforms could shed light on the mechanism of action of the Met66 and its impact on the development of neuropsychiatric-associated disorders. In the present study, we report the backbone 1 H, 13 C, and 15 N NMR assignments of both full-length Val66 and Met66 prodomains in the presence of 2 M urea. These conditions were utilized to suppress residual structure and aid subsequent native state structural investigations aimed at mapping and identifying variant-dependent conformational differences under native-state conditions.

Nuclear magnetic resonance studies on yeast tRNAPhe. II. Assignment of the iminoproton resonances of the anticodon and T stem by means of nuclear Overhauser effect experiments at 500 MHz.

PubMed Central

Heerschap, A; Haasnoot, C A; Hilbers, C W

1983-01-01

Resonances of the water exchangeable iminoprotons of the T and anticodon stem of yeast tRNAPhe were assigned by means of Nuclear Overhauser Effects (NOE's). Together with our previous assignments of iminoproton resonances from the acceptor and D stem (A. Heerschap, C.A.G. Haasnoot and C.W. Hilbers (1982) Nucleic Acids Res. 10, 6981-7000) the present results constitute a complete assignment of all resonances of iminoprotons involved in the secondary structure of yeast tRNAPhe with a reliability and spectral resolution not reached heretofore. Separate identification of the methylprotons in m5C40 and m5C49 was also possible due to specific NOE patterns in the lowfield part of the spectrum. Our experiments indicate that in solution the psi 39 residue in the anticodon stem is orientated in a syn conformation in contrast to the normally observed anti orientation of the uracil base in AU basepairs. Evidence is presented that in solution the acceptor stem is stacked upon the T stem. Furthermore, it turns out that in a similar way the anticodon stem forms a continuous stack with the D stem, but here the m2(2)G26 residue is located between the latter two stems (as is found in the X-ray crystal structure). The stacking of these stems is not strictly dependent on the presence of magnesium ions. NOE experiments show that these structural features are preserved when proceeding from a buffer with magnesium ions to a buffer without magnesium ions although differences in chemical shifts and NOE intensities indicate changes in the conformation of the tRNA. PMID:6346268

15N-CPMAS nuclear magnetic resonace spectroscopy and biological stability of soil organic nitrogen in whole soil and particle-size fractions

Treesearch

R.J. DiCosty; D.P. Weliky; S.J. Anderson; E.A. Paul

2003-01-01

Soil organic nitrogen was quantified by solid-state 15N cross-polarization nuclear magnetic resonance spectroscopy (NMR) during a 14-month laboratory incubation of a sandy loam soil amended with 15N-clover. In whole soil and particle-size fractions, the clover-derived N was always 85-90% amide, 5 10% guanidinium N of...

Solid-State 15N NMR of 15N-Labeled Nylon 6 and Nylon 11

DTIC Science & Technology

1990-05-22

S. Veeman, E. M. Menger, W. Ritchey, and E. de Boer, Macromolecules, 1979, 12, 924. 2. A. N. Garroway , W. M. Ritchey and W. B. Moniz, Macromolecules...S. Veeman and E. M. Menger, Bull. Magn. Reson., 1980, 2, 77. 26. D. L. VanderHart and A. N. Garroway , J. Chem. Phys., 1979, 71, 2773. 27. M. D

Residue selective 15N CEST and CPMG experiments for studies of millisecond timescale protein dynamics.

PubMed

Niu, Xiaogang; Ding, Jienv; Zhang, Wenbo; Li, Qianwen; Hu, Yunfei; Jin, Changwen

2018-06-01

Proteins are intrinsically dynamic molecules and undergo exchanges among multiple conformations to perform biological functions. The CPMG relaxation dispersion and CEST experiments are two important solution NMR techniques for characterizing the conformational exchange processes on the millisecond timescale. Traditional pseudo 3D 15 N CEST and CPMG experiments have certain limitations in their applications. For example, both experiments have low sensitivity for broadened resonances, and the process of optimizing sample conditions and experimental parameters are often time consuming. To overcome these limitations, we herein present a new set of residue selective 15 N CEST and CPMG pulse sequences by employing the Hartmann-Hahn cross-polarization transfer of magnetization in both 1D and 2D schemes. Combined with frequency labeling in the indirect dimension using only a small number of increments, the pulse sequences in the 2D scheme can be applied on resonances in overlapped regions of the 1 H- 15 N HSQC spectrum. The pulse sequences were further applied on several proteins, demonstrating their advantages over the traditional CEST and CPMG experiments under specific circumstances. Copyright © 2018 Elsevier Inc. All rights reserved.

Hyperpolarized 13 C,15 N2 -Urea MRI for assessment of the urea gradient in the porcine kidney.

PubMed

Hansen, Esben S S; Stewart, Neil J; Wild, Jim M; Stødkilde-Jørgensen, Hans; Laustsen, Christoffer

2016-12-01

A decline in cortico-medullary osmolality gradient of the kidney may serve as an early indicator of pathological disruption of the tubular reabsorption process. The purpose of this study was to investigate the feasibility of hyperpolarized 13 C, 15 N 2 -urea MRI as a biomarker of renal function in healthy porcine kidneys resembling the human physiology. Five healthy female Danish domestic pigs (weight 30 kg) were scanned at 3 Tesla (T) using a 13 C 3D balanced steady-state MR pulse sequence following injection of hyperpolarized 13 C, 15 N 2 -urea via a femoral vein catheter. Images were acquired at different time points after urea injection, and following treatment with furosemide. A gradient in cortico-medullary urea was observed with an intramedullary accumulation 75 s after injection of hyperpolarized 13 C, 15 N 2 -urea, whereas images acquired at earlier time points postinjection were dominated by cortical perfusion. Furosemide treatment resulted in an increased urea accumulation in the cortical space, leading to a reduction of the medullary-to-cortical signal ratio of 49%. This study demonstrates that hyperpolarized 13 C, 15 N 2 -urea MRI is capable of identifying the intrarenal accumulation of urea and can differentiate acute renal functional states in multipapillary kidneys, highlighting the potential for human translation. Magn Reson Med 76:1895-1899, 2016. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Temperature- and Length-Dependent Energetics of Formation for Polyalanine Helices in Water: Assignment of wAla(n,T) and Temperature-Dependent CD Ellipticity Standards

PubMed Central

Job, Gabriel E.; Kennedy, Robert J.; Heitmann, Björn; Miller, Justin S.; Walker, Sharon M.; Kemp*, Daniel S.

2006-01-01

Length-dependent helical propensities wAla(n,T) at T = 10, 25, and 60 °C are assigned from t/c values and NMR 13C chemical shifts for series 1 peptides TrpLysmInp2tLeu–AlantLeuInp2LysmNH2, n = 15, 19, and 25, m = 5, in water. Van’t Hoff analysis of wAla(n,T) show that α-helix formation is primarily enthalpy-driven. For series 2 peptides Ac–Trp Lys5Inp2tLeu–βAspHel–Alan–beta–tLeuInp2Lys5NH2, n = 12 and 22, which contain exceptionally helical Alan cores, protection factor-derived fractional helicities FH are assigned in the range 10–30 °C in water and used to calibrate temperature-dependent CD ellipticities [θ]λ,H,n,T. These are applied to CD data for series 1 peptides, 12 ≤ n ≤ 45, to confirm the wAla(n,T) assignments at T = 25 and 60 °C. The [θ]λ,H,n,T are temperature dependent within the wavelength region, 222 ± 12 nm, and yield a temperature correction for calculation of FH from experimental values of [θ]222,n,T,Exp. PMID:16787087

Effortless assignment with 4D covariance sequential correlation maps

NASA Astrophysics Data System (ADS)

Harden, Bradley J.; Mishra, Subrata H.; Frueh, Dominique P.

2015-11-01

Traditional Nuclear Magnetic Resonance (NMR) assignment procedures for proteins rely on preliminary peak-picking to identify and label NMR signals. However, such an approach has severe limitations when signals are erroneously labeled or completely neglected. The consequences are especially grave for proteins with substantial peak overlap, and mistakes can often thwart entire projects. To overcome these limitations, we previously introduced an assignment technique that bypasses traditional pick peaking altogether. Covariance Sequential Correlation Maps (COSCOMs) transform the indirect connectivity information provided by multiple 3D backbone spectra into direct (H, N) to (H, N) correlations. Here, we present an updated method that utilizes a single four-dimensional spectrum rather than a suite of three-dimensional spectra. We demonstrate the advantages of 4D-COSCOMs relative to their 3D counterparts. We introduce improvements accelerating their calculation. We discuss practical considerations affecting their quality. And finally we showcase their utility in the context of a 52 kDa cyclization domain from a non-ribosomal peptide synthetase.

Lineshape asymmetry for joint coherent population trapping and three-photon N resonances

NASA Astrophysics Data System (ADS)

Hancox, Cindy; Hohensee, Michael; Crescimanno, Michael; Phillips, David F.; Walsworth, Ronald L.

2008-06-01

We show that a characteristic two photon lineshape asymmetry arises in coherent population trapping (CPT) and three photon (N) resonances because both resonances are simultaneously induced by modulation sidebands in the interrogating laser light. The N resonance is a three-photon resonance in which a two-photon Raman excitation is combined with a resonant optical pumping field. This joint CPT and N resonance can be the dominant source of lineshape distortion, with direct relevance for the operation of miniaturized atomic frequency standards. We present the results of both an experimental study and theoretical treatment of the asymmetry of the joint CPT and N resonance under conditions typical to the operation of an N resonance clock.

Resonant photoluminescence studies of carrier localisation in c-plane InGaN/GaN quantum well structures

NASA Astrophysics Data System (ADS)

Blenkhorn, W. E.; Schulz, S.; Tanner, D. S. P.; Oliver, R. A.; Kappers, M. J.; Humphreys, C. J.; Dawson, P.

2018-05-01

In this paper we report on changes in the form of the low temperature (12 K) photoluminescence spectra of an InGaN/GaN quantum well structure as a function of excitation photon energy. As the photon energy is progressively reduced we observe at a critical energy a change in the form of the spectra from one which is determined by the occupation of the complete distribution of hole localisation centres to one which is determined by the resonant excitation of specific localisation sites. This change is governed by an effective mobility edge whereby the photo-excited holes remain localised at their initial energy and are prevented from scattering to other localisation sites. This assignment is confirmed by the results of atomistic tight binding calculations which show that the wave function overlap of the lowest lying localised holes with other hole states is low compared with the overlap of higher lying hole states with other higher lying hole states.

Resonance assignment of the NMR spectra of disordered proteins using a multi-objective non-dominated sorting genetic algorithm.

PubMed

Yang, Yu; Fritzsching, Keith J; Hong, Mei

2013-11-01

A multi-objective genetic algorithm is introduced to predict the assignment of protein solid-state NMR (SSNMR) spectra with partial resonance overlap and missing peaks due to broad linewidths, molecular motion, and low sensitivity. This non-dominated sorting genetic algorithm II (NSGA-II) aims to identify all possible assignments that are consistent with the spectra and to compare the relative merit of these assignments. Our approach is modeled after the recently introduced Monte-Carlo simulated-annealing (MC/SA) protocol, with the key difference that NSGA-II simultaneously optimizes multiple assignment objectives instead of searching for possible assignments based on a single composite score. The multiple objectives include maximizing the number of consistently assigned peaks between multiple spectra ("good connections"), maximizing the number of used peaks, minimizing the number of inconsistently assigned peaks between spectra ("bad connections"), and minimizing the number of assigned peaks that have no matching peaks in the other spectra ("edges"). Using six SSNMR protein chemical shift datasets with varying levels of imperfection that was introduced by peak deletion, random chemical shift changes, and manual peak picking of spectra with moderately broad linewidths, we show that the NSGA-II algorithm produces a large number of valid and good assignments rapidly. For high-quality chemical shift peak lists, NSGA-II and MC/SA perform similarly well. However, when the peak lists contain many missing peaks that are uncorrelated between different spectra and have chemical shift deviations between spectra, the modified NSGA-II produces a larger number of valid solutions than MC/SA, and is more effective at distinguishing good from mediocre assignments by avoiding the hazard of suboptimal weighting factors for the various objectives. These two advantages, namely diversity and better evaluation, lead to a higher probability of predicting the correct assignment for a

Box-modeling of 15N/14N in mammals.

PubMed

Balter, Vincent; Simon, Laurent; Fouillet, Hélène; Lécuyer, Christophe

2006-03-01

The 15N/14N signature of animal proteins is now commonly used to understand their physiology and quantify the flows of nutrient in trophic webs. These studies assume that animals are predictably 15N-enriched relative to their food, but the isotopic mechanism which accounts for this enrichment remains unknown. We developed a box model of the nitrogen isotope cycle in mammals in order to predict the 15N/14N ratios of body reservoirs as a function of time, N intake and body mass. Results of modeling show that a combination of kinetic isotope fractionation during the N transfer between amines and equilibrium fractionation related to the reversible conversion of N-amine into ammonia is required to account for the well-established approximately 4 per thousand 15N-enrichment of body proteins relative to the diet. This isotopic enrichment observed in proteins is due to the partial recycling of 15N-enriched urea and the urinary excretion of a fraction of the strongly 15N-depleted ammonia reservoir. For a given body mass and diet delta15N, the isotopic compositions are mainly controlled by the N intake. Increase of the urea turnover combined with a decrease of the N intake lead to calculate a delta15N increase of the proteins, in agreement with the observed increase of collagen delta15N of herbivorous animals with aridity. We further show that the low delta15N collagen values of cave bears cannot be attributed to the dormancy periods as it is commonly thought, but inversely to the hyperphagia behavior. This model highlights the need for experimental investigations performed with large mammals in order to improve our understanding of natural variations of delta15N collagen.

Generalized topology for resonators having N commensurate harmonics

NASA Astrophysics Data System (ADS)

Danzi, Francesco; Gibert, James M.; Frulla, Giacomo; Cestino, Enrico

2018-04-01

Despite the ubiquity of both linear and nonlinear multimember resonators in MEMS and kinetic energy harvesting devices very few research efforts examine the orientation of members in the resonator on its dynamic behavior. Previous efforts to design this type of resonator constrains the members to have relative orientations that are 0○ or 90○ to each other, i.e., the elements are connected inline with adjoining members or are perpendicular to adjoining members. The work expands upon the existing body of research by considering the effect of the relative orientation between members on the dynamic behavior of the system. In this manuscript, we derive a generalized reduced-order model for the design of a multi-member planar resonator that has integer multiple modal frequencies. The model is based on a Rayleigh Ritz approximation where the number of degrees of freedom equals the number of structural members in the resonator. The analysis allows the generation of design curves, representing all the possible solutions for modal frequencies that are commensurate. The generalized model, valid for an N-DOF structure, is then restricted for a 2- and 3-DOF system/member resonator, where the linear dynamic behavior of the resonator is investigated in depth. Furthermore, this analysis demonstrates a rule of thumb; relaxing restrictions on the relative orientation of members in a planar structure, allows the structure to exhibit exactly N commensurable frequencies if it contains N members.

Coupled-channel model for K ¯ N scattering in the resonant region

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fernández-Ramírez, Cesar; Danilkin, Igor V.; Manley, D. Mark

2016-02-18

Here, we present a unitary multichannel model formore » $$\\bar{K}$$N scattering in the resonance region that fulfills unitarity. It has the correct analytical properties for the amplitudes once they are extended to the complex-$s$ plane and the partial waves have the right threshold behavior. In order to determine the parameters of the model, we have fitted single-energy partial waves up to J = 7/2 and up to 2.15 GeV of energy in the center-of-mass reference frame obtaining the poles of the Λ* and Σ* resonances, which are compared to previous analyses. Furthermore, we provide the most comprehensive picture of the S = –1 hyperon spectrum to date. Here, important differences are found between the available analyses making the gathering of further experimental information on $$\\bar{K}$$N scattering mandatory to make progress in the assessment of the hyperon spectrum.« less

Recording 13C-15N HMQC 2D sparse spectra in solids in 30 s

NASA Astrophysics Data System (ADS)

Kupče, Ēriks; Trébosc, Julien; Perrone, Barbara; Lafon, Olivier; Amoureux, Jean-Paul

2018-03-01

We propose a dipolar HMQC Hadamard-encoded (D-HMQC-Hn) experiment for fast 2D correlations of abundant nuclei in solids. The main limitation of the Hadamard methods resides in the length of the encoding pulses, which results from a compromise between the selectivity and the sensitivity due to losses. For this reason, these methods should mainly be used with sparse spectra, and they profit from the increased separation of the resonances at high magnetic fields. In the case of the D-HMQC-Hn experiments, we give a simple rule that allows directly setting the optimum length of the selective pulses, versus the minimum separation of the resonances in the indirect dimension. The demonstration has been performed on a fully 13C,15N labelled f-MLF sample, and it allowed recording the build-up curves of the 13C-15N cross-peaks within 10 min. However, the method could also be used in the case of less sensitive samples, but with more accumulations.

IR Spectra of n-Bu4M (M = Si, Ge, Sn, Pb), n-BuAuPPh3-d15, and "n-Bu" on a Gold Surface.

PubMed

Kaleta, Jiří; Bednárová, Lucie; Čížková, Martina; Wen, Jin; Kaletová, Eva; Michl, Josef

2017-06-22

Observed and DFT-calculated IR spectra of n-Bu 4 M (M = Si, Ge, Sn, Pb), (CH 3 CH 2 CH 2 13 CD 2 ) 4 Sn, and n-BuAuPPh 3 -d 15 are reported and assigned. The asymmetric CH stretching vibration of the CH 2 group adjacent to the metal atom appears as a distinct shoulder at ∼2934 cm -1 , whereas for other CH 2 groups it is located at ∼2922 cm -1 . The characteristic peak at ∼2899 cm -1 is attributed to an overtone of a symmetric CH 2 bend at ∼1445 cm -1 . In n-BuAuPPh 3 -d 15 , the CH stretching vibrations of the butyl group are shifted to lower frequencies by ∼10 cm -1 , and two possible rationalizations are offered.

Effortless assignment with 4D covariance sequential correlation maps.

PubMed

Harden, Bradley J; Mishra, Subrata H; Frueh, Dominique P

2015-11-01

Traditional Nuclear Magnetic Resonance (NMR) assignment procedures for proteins rely on preliminary peak-picking to identify and label NMR signals. However, such an approach has severe limitations when signals are erroneously labeled or completely neglected. The consequences are especially grave for proteins with substantial peak overlap, and mistakes can often thwart entire projects. To overcome these limitations, we previously introduced an assignment technique that bypasses traditional pick peaking altogether. Covariance Sequential Correlation Maps (COSCOMs) transform the indirect connectivity information provided by multiple 3D backbone spectra into direct (H, N) to (H, N) correlations. Here, we present an updated method that utilizes a single four-dimensional spectrum rather than a suite of three-dimensional spectra. We demonstrate the advantages of 4D-COSCOMs relative to their 3D counterparts. We introduce improvements accelerating their calculation. We discuss practical considerations affecting their quality. And finally we showcase their utility in the context of a 52 kDa cyclization domain from a non-ribosomal peptide synthetase. Copyright © 2015 Elsevier Inc. All rights reserved.

15N NATURAL ABUNDANCE AND 15N LABELLING STUDIES IN FOREST ECOSYSTEMS

EPA Science Inventory

The relative amounts of the two stable isotopes of Nitrogen (N), 15N, and N, vary predictably in soils and plant tissues of forests and other non-cultivated ecosystems. light fractionations, or discriminations against the heavier N isotope, that can occur as N cycles through vege...

New astrophysical S factor for the {sup 15}N(p,{gamma}){sup 16}O reaction via the asymptotic normalization coefficient (ANC) method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mukhamedzhanov, A. M.; Gagliardi, C. A.; Goldberg, V. Z.

2008-07-15

The {sup 15}N(p,{gamma}){sup 16}O reaction provides a path from the CN cycle to the CNO bi-cycle and CNO tri-cycle. The measured astrophysical factor for this reaction is dominated by resonant capture through two strong J{sup {pi}}=1{sup -} resonances at E{sub R}=312 and 962 keV and direct capture to the ground state. Asymptotic normalization coefficients (ANCs) for the ground and seven excited states in {sup 16}O were extracted from the comparison of experimental differential cross sections for the {sup 15}N({sup 3}He,d){sup 16}O reaction with distorted-wave Born approximation calculations. Using these ANCs and proton and {alpha} resonance widths determined from an R-matrixmore » fit to the data from the {sup 15}N(p,{alpha}){sup 12}C reaction, we carried out an R-matrix calculation to obtain the astrophysical factor for the {sup 15}N(p,{gamma}){sup 16}O reaction. The results indicate that the direct capture contribution was previously overestimated. We find the astrophysical factor to be S(0)=36.0{+-}6.0 keV b, which is about a factor of 2 lower than the presently accepted value. We conclude that for every 2200{+-}300 cycles of the main CN cycle one CN catalyst is lost due to this reaction.« less

Towards unsupervised polyaromatic hydrocarbons structural assignment from SA-TIMS-FTMS data.

PubMed

Benigni, Paolo; Marin, Rebecca; Fernandez-Lima, Francisco

2015-10-01

With the advent of high resolution ion mobility analyzers and their coupling to ultrahigh resolution mass spectrometers, there is a need to further develop a theoretical workflow capable of correlating experimental accurate mass and mobility measurements with tridimensional candidate structures. In the present work, a general workflow is described for unsupervised tridimensional structural assignment based on accurate mass measurements, mobility measurements, in silico 2D-3D structure generation, and theoretical mobility calculations. In particular, the potential of this workflow will be shown for the analysis of polyaromatic hydrocarbons from Coal Tar SRM 1597a using selected accumulation - trapped ion mobility spectrometry (SA-TIMS) coupled to Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS). The proposed workflow can be adapted to different IMS scenarios, can utilize different collisional cross-section calculators and has the potential to include MS n and IMS n measurements for faster and more accurate tridimensional structural assignment.

Experimental and calculated 1H, 13C, 15N NMR spectra of famotidine

NASA Astrophysics Data System (ADS)

Barańska, M.; Czarniecki, K.; Proniewicz, L. M.

2001-05-01

Famotidine, 3-[[[2-[(aminoiminomethyl)amino]-4-thiazolyl]methyl]thio]- N-(aminosulfonyl), is a histamine H 2-receptor blocker that has been used mainly for the treatment of peptic ulcers and the Zollinger-Ellison syndrome. Its NMR spectra in different solvents were reported earlier; however, detailed interpretation has not been done thus far. In this work, experimental 1H, 13C and 15N NMR spectra of famotidine dissolved in DMSO-d 6 are shown. The assignment of observed chemical shifts is based on quantum chemical calculation at the Hartree-Fock/6-31G ∗ level. The geometry optimization of the famotidine molecule with two internal hydrogen bonds, i.e. [N(3)-H(23)⋯N(9) and N(3)⋯H(34)-N(20)], is done by using the B3LYP method with the 6-31G ∗ basis set.

Amide or Amine: Determining the Origin of the 3300 cm−1 NH Mode in Protein SFG Spectra Using 15N Isotope Labels

PubMed Central

Weidner, Tobias; Breen, Nicholas F.; Drobny, Gary P.; Castner, David G.

2009-01-01

Sum frequency generation (SFG) vibrational spectroscopy has been employed in biomaterials research and protein adsorption studies with growing success in recent years. A number of studies focusing on understanding SFG spectra of proteins and peptides at different interfaces have laid the foundation for future, more complex studies. In many cases a strong NH mode near 3300 cm−1 is observed in the SFG spectra, but the relationship of this mode to the peptide structure is uncertain since it has been assigned to either a backbone amide mode or a side chain related amine resonance. A thorough understanding of the SFG spectra of these first model systems is an important first step for future experiments. To clarify the origin of the NH SFG mode we studied 15N isotopically labeled 14-amino acid amphiphilic model peptides composed of lysine (K) and leucine (L) in an α-helical secondary structure (LKα14) that were adsorbed onto charged surfaces in situ at the solid-liquid interface. 15N substitution at the terminal amine group of the lysine side chains resulted in a red-shift of the NH mode of 9 cm−1 on SiO2 and 13 cm−1 on CaF2. This clearly shows the 3300 cm−1 NH feature is associated with side chain NH stretches and not with backbone amide modes. PMID:19873996

Amide or amine: determining the origin of the 3300 cm(-1) NH mode in protein SFG spectra using 15N isotope labels.

PubMed

Weidner, Tobias; Breen, Nicholas F; Drobny, Gary P; Castner, David G

2009-11-26

Sum frequency generation (SFG) vibrational spectroscopy has been employed in biomaterials research and protein adsorption studies with growing success in recent years. A number of studies focusing on understanding SFG spectra of proteins and peptides at different interfaces have laid the foundation for future, more complex studies. In many cases, a strong NH mode near 3300 cm(-1) is observed in the SFG spectra, but the relationship of this mode to the peptide structure is uncertain, since it has been assigned to either a backbone amide mode or a side chain related amine resonance. A thorough understanding of the SFG spectra of these first model systems is an important first step for future experiments. To clarify the origin of the NH SFG mode, we studied (15)N isotopically labeled 14-amino acid amphiphilic model peptides composed of lysine (K) and leucine (L) in an alpha-helical secondary structure (LKalpha14) that were adsorbed onto charged surfaces in situ at the solid-liquid interface. (15)N substitution at the terminal amine group of the lysine side chains resulted in a red-shift of the NH mode of 9 cm(-1) on SiO(2) and 13 cm(-1) on CaF(2). This clearly shows the 3300 cm(-1) NH feature is associated with side chain NH stretches and not with backbone amide modes.

Influence of InGaN sub-quantum-well on performance of InAlN/GaN/InAlN resonant tunneling diodes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Haoran; Yang, Lin'an, E-mail: layang@xidian.edu.cn; Hao, Yue

The resonant tunneling mechanism of the GaN based resonant tunneling diode (RTD) with an InGaN sub-quantum-well has been investigated by means of numerical simulation. At resonant-state, Electrons in the InGaN/InAlN/GaN/InAlN RTD tunnel from the emitter region through the aligned discrete energy levels in the InGaN sub-quantum-well and GaN main-quantum-well into the collector region. The implantation of the InGaN sub-quantum-well alters the dominant transport mechanism, increase the transmission coefficient and give rise to the peak current and peak-to-valley current ratio. We also demonstrate that the most pronounced negative-differential-resistance characteristic can be achieved by choosing appropriately the In composition of In{sub x}Ga{submore » 1−x}N at around x = 0.06.« less

Chemical Assignment of Structural Isomers of Sulfur-Containing Metabolites in Garlic by Liquid Chromatography-Fourier Transform Ion Cyclotron Resonance-Mass Spectrometry.

PubMed

Nakabayashi, Ryo; Sawada, Yuji; Aoyagi, Morihiro; Yamada, Yutaka; Hirai, Masami Yokota; Sakurai, Tetsuya; Kamoi, Takahiro; Rowan, Daryl D; Saito, Kazuki

2016-02-01

The chemical assignment of metabolites is crucial to understanding the relation between food composition and biological activity. This study was designed to detect and chemically assign sulfur-containing metabolites by using LC-Fourier transform ion cyclotron resonance-mass spectrometry (FTICR-MS) in Allium plants. Ultrahigh resolution (>250,000 full width at half-maximum) and mass accuracy (<1 mDa) by FTICR-MS allowed us to distinguish ions containing sulfur isotopes ((32)S and (34)S). Putative 69 S-containing monoisotopic ions (S-ions) were extracted from the metabolome data of onion (Allium cepa), green onion (Allium fistulosum), and garlic (Allium sativum) on the basis of theoretical mass differences between (32)S-ions and their (34)S-substituted counterparts and on the natural abundance of (34)S. Eight S-ions were chemically assigned by using the reference data according to the guidelines of the Metabolomics Standards Initiative. Three ions detected in garlic were assigned as derived from the isomers γ-glutamyl-S-1-propenylcysteine and γ-glutamyl-S-2-propenylcysteine and as S-2-propenylmercaptoglutathione on the basis of differences in key product ions identified in reference tandem MS spectra. The ability to discriminate between such geometric isomers will be extremely useful for the chemical assignment of unknown metabolites in MS-based metabolomics. © 2016 American Society for Nutrition.

32 CFR Appendix B to Part 150 - Format for Assignment of Errors and Brief on Behalf of Accused (§ 150.15)

Code of Federal Regulations, 2013 CFR

2013-07-01

... 32 National Defense 1 2013-07-01 2013-07-01 false Format for Assignment of Errors and Brief on Behalf of Accused (§ 150.15) B Appendix B to Part 150 National Defense Department of Defense OFFICE OF... OF PRACTICE AND PROCEDURE Pt. 150, App. B Appendix B to Part 150—Format for Assignment of Errors and...

32 CFR Appendix B to Part 150 - Format for Assignment of Errors and Brief on Behalf of Accused (§ 150.15)

Code of Federal Regulations, 2011 CFR

2011-07-01

... 32 National Defense 1 2011-07-01 2011-07-01 false Format for Assignment of Errors and Brief on Behalf of Accused (§ 150.15) B Appendix B to Part 150 National Defense Department of Defense OFFICE OF... OF PRACTICE AND PROCEDURE Pt. 150, App. B Appendix B to Part 150—Format for Assignment of Errors and...

Chemoselective detection and discrimination of carbonyl-containing compounds in metabolite mixtures by 1H-detected 15N NMR

PubMed Central

Lane, Andrew N.; Arumugam, Sengodagounder; Lorkiewicz, Pawel K.; Higashi, Richard M.; Laulhé, Sébastien; Nantz, Michael H.; Moseley, Hunter N.B.; Fan, Teresa W.-M.

2015-01-01

NMR spectra of mixtures of metabolites extracted from cells or tissues are extremely complex, reflecting the large number of compounds that are present over a wide range of concentrations. Although multidimensional NMR can greatly improve resolution as well as improve reliability of compound assignments, lower abundance metabolites often remain hidden. We have developed a carbonyl selective aminooxy probe that specifically reacts with free keto and aldehyde functions, but not carboxylates. By incorporating 15N in the aminooxy functional group, 15N-edited NMR was used to select exclusively those metabolites that contain a free carbonyl function while all other metabolites are rejected. Here we demonstrate that the chemical shifts of the aminooxy adducts of ketones and aldehydes are very different, which can be used to discriminate between aldoses and ketoses for example. Utilizing the 2 or 3 bond 15N-1H couplings, the 15N-edited NMR analysis was optimized first with authentic standards and then applied to an extract of the lung adenocarcinoma cell line A549. More than 30 carbonyl containing compounds at NMR detectable levels, 6 of which we have assigned by reference to our database. As the aminooxy probe contains a permanently charged quaternary ammonium group, the adducts are also optimized for detection by mass spectrometry. Thus, this sample preparation technique provides a better link between the two structural determination tools, thereby paving the way to faster and more reliable identification of both known and unknown metabolites directly in crude biological extracts. PMID:25616249

Covariance NMR Processing and Analysis for Protein Assignment.

PubMed

Harden, Bradley J; Frueh, Dominique P

2018-01-01

During NMR resonance assignment it is often necessary to relate nuclei to one another indirectly, through their common correlations to other nuclei. Covariance NMR has emerged as a powerful technique to correlate such nuclei without relying on error-prone peak peaking. However, false-positive artifacts in covariance spectra have impeded a general application to proteins. We recently introduced pre- and postprocessing steps to reduce the prevalence of artifacts in covariance spectra, allowing for the calculation of a variety of 4D covariance maps obtained from diverse combinations of pairs of 3D spectra, and we have employed them to assign backbone and sidechain resonances in two large and challenging proteins. In this chapter, we present a detailed protocol describing how to (1) properly prepare existing 3D spectra for covariance, (2) understand and apply our processing script, and (3) navigate and interpret the resulting 4D spectra. We also provide solutions to a number of errors that may occur when using our script, and we offer practical advice when assigning difficult signals. We believe such 4D spectra, and covariance NMR in general, can play an integral role in the assignment of NMR signals.

Current-Tunable NbTiN Coplanar Photonic Bandgap Resonators

NASA Astrophysics Data System (ADS)

Asfaw, A.; Sigillito, A. J.; Tyryshkin, A. M.; Lyon, S. A.

Coplanar waveguide resonators have been used in several experimental settings, from superconducting qubits to electron spin resonance. In our particular application of electron spin resonance, these resonators provide increased sensitivity to electron spins due to the small mode volume. Experiments have shown that these resonators can be used to readout as few as 300 spins per shot. Recently, photonic bandgap resonators have been shown to extend the advantages of traditional CPW resonators by allowing spin manipulation both at microwave and radio frequencies, thereby enabling both electron and nuclear spin resonance within the same resonator. We present measurements made using photonic bandgap resonators fabricated with thin NbTiN films which demonstrate microwave tunability of the resonator by modulating the kinetic inductance of the superconductor. Driving a small direct current through the center pin of the resonator allows us to tune the resonant frequency by over 30 MHz around 6.4 GHz while maintaining a quality factor over 8000 at 4.8K. This provides fast and simple tunability of coplanar waveguide resonators and opens new possibilities for multiple frequency electron spin resonance experiments.

Rapid measurement of 3J(H N-H alpha) and 3J(N-H beta) coupling constants in polypeptides.

PubMed

Barnwal, Ravi Pratap; Rout, Ashok K; Chary, Kandala V R; Atreya, Hanudatta S

2007-12-01

We present two NMR experiments, (3,2)D HNHA and (3,2)D HNHB, for rapid and accurate measurement of 3J(H N-H alpha) and 3J(N-H beta) coupling constants in polypeptides based on the principle of G-matrix Fourier transform NMR spectroscopy and quantitative J-correlation. These experiments, which facilitate fast acquisition of three-dimensional data with high spectral/digital resolution and chemical shift dispersion, will provide renewed opportunities to utilize them for sequence specific resonance assignments, estimation/characterization of secondary structure with/without prior knowledge of resonance assignments, stereospecific assignment of prochiral groups and 3D structure determination, refinement and validation. Taken together, these experiments have a wide range of applications from structural genomics projects to studying structure and folding in polypeptides.

13C-13C dipolar recoupling under very fast magic angle spinning in solid-state nuclear magnetic resonance: Applications to distance measurements, spectral assignments, and high-throughput secondary-structure determination

NASA Astrophysics Data System (ADS)

Ishii, Yoshitaka

2001-05-01

A technique is presented to recouple homonuclear dipolar couplings between dilute spin pairs such as 13C-13C systems under very fast magic angle spinning (MAS) in solid-state nuclear magnetic resonance (NMR) spectroscopy. The presented technique, finite pulse rf driven recoupling (fpRFDR), restores homonuclear dipolar interactions based on constructive usage of finite pulse-width effects in a phase- and symmetry-cycled π-pulse train in which a rotor-synchronous π pulse is applied every rotation period. The restored effective dipolar interaction has the form of a zero-quantum dipolar Hamiltonian for static solids, whose symmetry in spin space is different from that obtained by conventional rf driven recoupling (RFDR) techniques. It is demonstrated that the efficiency of recoupling by fpRFDR is not strongly dependent on chemical shift differences or resonance offsets in contrast to previous recoupling methods under very fast MAS. To realize distance measurements without effects of spin relaxation, a constant-time version of fpRFDR (CT-fpRFDR) is introduced, in which the effective evolution period is varied by refocusing dipolar evolution with a rotor-synchronized solid echo while the total recoupling period is kept constant. From CT-fpRFDR experiments at a spinning speed of 30.3 kHz in a field of 17.6 T, the 13C-13C distance of [1-13C]Ala-[1-13C]Gly-Gly was determined to be 3.27 Å, which agrees well with the value of 3.20 Å obtained by x-ray diffraction. Also, two-dimensional (2D) 13C/13C chemical-shift correlation NMR spectrum in a field of 9.4 T was obtained with fpRFDR for fibrils of the segmentally 13C- and 15N-labeled Alzheimer's β-Amyloid fragments, Aβ16-22 (residues 16-22 taken from the 40-residue Aβ peptide) in which Leu-17 through Ala-21 are uniformly 13C- and 15N-labeled. Most 13C resonances for the main chain as well as for the side chains are assigned based on 2D 13C/13C chemical-shift correlation patterns specific to amino-acid types. Examination

13C and (15)N chemical shift tensors in adenosine, guanosine dihydrate, 2'-deoxythymidine, and cytidine.

PubMed

Stueber, Dirk; Grant, David M

2002-09-04

The (13)C and (15)N chemical shift tensor principal values for adenosine, guanosine dihydrate, 2'-deoxythymidine, and cytidine are measured on natural abundance samples. Additionally, the (13)C and (15)N chemical shielding tensor principal values in these four nucleosides are calculated utilizing various theoretical approaches. Embedded ion method (EIM) calculations improve significantly the precision with which the experimental principal values are reproduced over calculations on the corresponding isolated molecules with proton-optimized geometries. The (13)C and (15)N chemical shift tensor orientations are reliably assigned in the molecular frames of the nucleosides based upon chemical shielding tensor calculations employing the EIM. The differences between principal values obtained in EIM calculations and in calculations on isolated molecules with proton positions optimized inside a point charge array are used to estimate the contributions to chemical shielding arising from intermolecular interactions. Moreover, the (13)C and (15)N chemical shift tensor orientations and principal values correlate with the molecular structure and the crystallographic environment for the nucleosides and agree with data obtained previously for related compounds. The effects of variations in certain EIM parameters on the accuracy of the shielding tensor calculations are investigated.

Fabrication and characterization of GaN nanowire doubly clamped resonators

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maliakkal, Carina B., E-mail: carina@tifr.res.in; Mathew, John P.; Hatui, Nirupam

2015-09-21

Gallium nitride (GaN) nanowires (NWs) have been intensely researched as building blocks for nanoscale electronic and photonic device applications; however, the mechanical properties of GaN nanostructures have not been explored in detail. The rigidity, thermal stability, and piezoelectric properties of GaN make it an interesting candidate for nano-electromechanical systems. We have fabricated doubly clamped GaN NW electromechanical resonators on sapphire using electron beam lithography and estimated the Young's modulus of GaN from resonance frequency measurements. For wires of triangular cross section with side ∼90 nm, we obtained values for the Young's modulus to be about 218 and 691 GPa, which are ofmore » the same order of magnitude as the values reported for bulk GaN. We also discuss the role of residual strain in the nanowire on the resonant frequency and the orientation dependence of the Young's modulus in wurtzite crystals.« less

Constraining the S factor of {sup 15}N(p,{gamma}){sup 16}O at astrophysical energies

DOE Office of Scientific and Technical Information (OSTI.GOV)

LeBlanc, P. J.; Goerres, J.; Beard, M.

2010-11-15

The {sup 15}N(p,{gamma}){sup 16}O reaction represents a breakout reaction linking the first and second cycles of the CNO cycles redistributing the carbon and nitrogen abundances into the oxygen range. The reaction is dominated by two broad resonances, at E{sub p}=338 and 1028 keV, and a direct capture contribution to the ground state of {sup 16}O. Interference effects between these contributions both in the low-energy region (E{sub p}<338 keV) and between the two resonances (33815}N(p,{gamma}){sup 16}O reaction has been remeasured coveringmore » the energy range from E{sub p}=1800 keV down to 130 keV. The results have been analyzed in the framework of a multilevel R-matrix theory and an S(0) value of 39.6 keV b has been found.« less

Si /SiGe n-type resonant tunneling diodes fabricated using in situ hydrogen cleaning

NASA Astrophysics Data System (ADS)

Suet, Z.; Paul, D. J.; Zhang, J.; Turner, S. G.

2007-05-01

In situ hydrogen cleaning to reduce the surface segregation of n-type dopants in SiGe epitaxy has been used to fabricate Si /SiGe resonant tunneling diodes in a joint gas source chemical vapor deposition and molecular beam epitaxial system. Diodes fabricated without the in situ clean demonstrate linear current-voltage characteristics, while a 15min hydrogen clean produces negative differential resistance with peak-to-valley current ratios up to 2.2 and peak current densities of 5.0A/cm2 at 30K. Analysis of the valley current and the band structure of the devices suggest methods for increasing the operating temperature of Si /SiGe resonant tunneling diodes as required for applications.

The contamination of commercial 15N2 gas stocks with 15N-labeled nitrate and ammonium and consequences for nitrogen fixation measurements.

PubMed

Dabundo, Richard; Lehmann, Moritz F; Treibergs, Lija; Tobias, Craig R; Altabet, Mark A; Moisander, Pia H; Granger, Julie

2014-01-01

We report on the contamination of commercial 15-nitrogen (15N) N2 gas stocks with 15N-enriched ammonium, nitrate and/or nitrite, and nitrous oxide. 15N2 gas is used to estimate N2 fixation rates from incubations of environmental samples by monitoring the incorporation of isotopically labeled 15N2 into organic matter. However, the microbial assimilation of bioavailable 15N-labeled N2 gas contaminants, nitrate, nitrite, and ammonium, is liable to lead to the inflation or false detection of N2 fixation rates. 15N2 gas procured from three major suppliers was analyzed for the presence of these 15N-contaminants. Substantial concentrations of 15N-contaminants were detected in four Sigma-Aldrich 15N2 lecture bottles from two discrete batch syntheses. Per mole of 15N2 gas, 34 to 1900 µmoles of 15N-ammonium, 1.8 to 420 µmoles of 15N-nitrate/nitrite, and ≥21 µmoles of 15N-nitrous oxide were detected. One 15N2 lecture bottle from Campro Scientific contained ≥11 µmoles of 15N-nitrous oxide per mole of 15N2 gas, and no detected 15N-nitrate/nitrite at the given experimental 15N2 tracer dilutions. Two Cambridge Isotopes lecture bottles from discrete batch syntheses contained ≥0.81 µmoles 15N-nitrous oxide per mole 15N2, and trace concentrations of 15N-ammonium and 15N-nitrate/nitrite. 15N2 gas equilibrated cultures of the green algae Dunaliella tertiolecta confirmed that the 15N-contaminants are assimilable. A finite-differencing model parameterized using oceanic field conditions typical of N2 fixation assays suggests that the degree of detected 15N-ammonium contamination could yield inferred N2 fixation rates ranging from undetectable, <0.01 nmoles N L(-1) d(-1), to 530 nmoles N L(-1) d(-1), contingent on experimental conditions. These rates are comparable to, or greater than, N2 fixation rates commonly detected in field assays. These results indicate that past reports of N2 fixation should be interpreted with caution, and demonstrate that the purity of commercial 15N2

Heteronuclear NMR assignments and secondary structure of the coiled coil trimerization domain from cartilage matrix protein in oxidized and reduced forms.

PubMed Central

Wiltscheck, R.; Kammerer, R. A.; Dames, S. A.; Schulthess, T.; Blommers, M. J.; Engel, J.; Alexandrescu, A. T.

1997-01-01

The C-terminal oligomerization domain of chicken cartilage matrix protein is a trimeric coiled coil comprised of three identical 43-residue chains. NMR spectra of the protein show equivalent magnetic environments for each monomer, indicating a parallel coiled coil structure with complete threefold symmetry. Sequence-specific assignments for 1H-, 15N-, and 13C-NMR resonances have been obtained from 2D 1H NOESY and TOCSY spectra, and from 3D HNCA, 15N NOESY-HSQC, and HCCH-TOCSY spectra. A stretch of alpha-helix encompassing five heptad repeats (35 residues) has been identified from intra-chain HN-HN and HN-H alpha NOE connectivities. 3JHNH alpha coupling constants, and chemical shift indices. The alpha-helix begins immediately downstream of inter-chain disulfide bonds between residues Cys 5 and Cys 7, and extends to near the C-terminus of the molecule. The threefold symmetry of the molecule is maintained when the inter-chain disulfide bonds that flank the N-terminus of the coiled coil are reduced. Residues Ile 21 through Glu 36 show conserved chemical shifts and NOE connectivities, as well as strong protection from solvent exchange in the oxidized and reduced forms of the protein. By contrast, residues Ile 10 through Val 17 show pronounced chemical shift differences between the oxidized and reduced protein. Strong chemical exchange NOEs between HN resonances and water indicate solvent exchange on time scales faster than 10 s, and suggests a dynamic fraying of the N-terminus of the coiled coil upon reduction of the disulfide bonds. Possible roles for the disulfide crosslinks of the oligomerization domain in the function of cartilage matrix protein are proposed. PMID:9260286

15 CFR 30.63 - Office of Management and Budget control numbers assigned pursuant to the Paperwork Reduction Act.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 15 Commerce and Foreign Trade 1 2010-01-01 2010-01-01 false Office of Management and Budget control numbers assigned pursuant to the Paperwork Reduction Act. 30.63 Section 30.63 Commerce and Foreign... FOREIGN TRADE REGULATIONS General Administrative Provisions § 30.63 Office of Management and Budget...

Stereospecific assignment of the asparagine and glutamine sidechain amide protons in proteins from chemical shift analysis.

PubMed

Harsch, Tobias; Schneider, Philipp; Kieninger, Bärbel; Donaubauer, Harald; Kalbitzer, Hans Robert

2017-02-01

Side chain amide protons of asparagine and glutamine residues in random-coil peptides are characterized by large chemical shift differences and can be stereospecifically assigned on the basis of their chemical shift values only. The bimodal chemical shift distributions stored in the biological magnetic resonance data bank (BMRB) do not allow such an assignment. However, an analysis of the BMRB shows, that a substantial part of all stored stereospecific assignments is not correct. We show here that in most cases stereospecific assignment can also be done for folded proteins using an unbiased artificial chemical shift data base (UACSB). For a separation of the chemical shifts of the two amide resonance lines with differences ≥0.40 ppm for asparagine and differences ≥0.42 ppm for glutamine, the downfield shifted resonance lines can be assigned to H δ21 and H ε21 , respectively, at a confidence level >95%. A classifier derived from UASCB can also be used to correct the BMRB data. The program tool AssignmentChecker implemented in AUREMOL calculates the Bayesian probability for a given stereospecific assignment and automatically corrects the assignments for a given list of chemical shifts.

First measurement of the double spin asymmetry in (-->)e(-->)p-->e(prime)pi(+)n in the resonance region.

PubMed

De Vita, R; Anghinolfi, M; Burkert, V D; Dodge, G E; Minehart, R; Taiuti, M; Weller, H; Adams, G; Amaryan, M J; Anciant, E; Armstrong, D S; Asavapibhop, B; Asryan, G; Audit, G; Auger, T; Avakian, H; Bagdasaryan, H; Ball, J P; Barrow, S; Battaglieri, M; Beard, K; Bektasoglu, M; Bianchi, N; Biselli, A S; Boiarinov, S; Bonner, B E; Bosted, P; Bouchigny, S; Branford, D; Brooks, W K; Bueltmann, S; Calarco, J R; Capitani, G P; Carman, D S; Carnahan, B; Cazes, A; Ciciani, L; Cole, P L; Coleman, A; Connelly, J; Cords, D; Corvisiero, P; Crabb, D; Crannell, H; Cummings, J P; De Sanctis, E; Degtyarenko, P V; Demirchyan, R; Denizli, H; Dennis, L; Dharmawardane, K V; Dhuga, K S; Djalali, C; Doughty, D; Dragovitsch, P; Dugger, M; Dytman, S; Eckhause, M; Egiyan, H; Egiyan, K S; Elouadrhiri, L; Empl, A; Farhi, L; Fatemi, R; Feuerbach, R J; Ficenec, J; Forest, T A; Frolov, V; Funsten, H; Gaff, S J; Gai, M; Garçon, M; Gavalian, G; Gilad, S; Gilfoyle, G P; Giovanetti, K L; Girard, P; Golovatch, E; Griffioen, K; Guidal, M; Guillo, M; Gyurjyan, V; Hadjidakis, C; Hancock, D; Hardie, J; Heddle, D; Heimberg, P; Hersman, F W; Hicks, K; Hicks, R S; Holtrop, M; Hu, J; Hyde-Wright, C E; Ishkanov, B S; Ito, M M; Jenkins, D; Joo, K; Kelley, J H; Kellie, J D; Khandaker, M; Kim, K Y; Kim, K; Kim, W; Klein, A; Klein, F J; Klusman, M; Kossov, M; Kramer, L H; Kuang, Y; Kuhn, S E; Lachniet, J; Laget, J M; Lawrence, D; Li, Ji; Livingston, K; Longhi, A; Loukachine, K; Lucas, M; Major, W; Manak, J J; Marchand, C; McAleer, S; McCarthy, J; McNabb, J W C; Mecking, B A; Mestayer, M D; Meyer, C A; Mikhailov, K; Mirazita, M; Miskimen, R; Mokeev, V; Muccifora, V; Mueller, J; Mutchler, G S; Napolitano, J; Nelson, S O; Niculescu, G; Niculescu, I; Niczyporuk, B B; Niyazov, R A; Opper, A K; O'Rielly, G V; Osipenko, M; Park, K; Pasyuk, E; Peterson, G; Philips, S A; Pivnyuk, N; Pocanic, D; Pogorelko, O; Polli, E; Pozdniakov, S; Preedom, B M; Price, J W; Prok, Y; Protopopescu, D; Qin, L M; Raue, B A; Reolon, A R; Riccardi, G; Ricco, G; Ripani, M; Ritchie, B G; Rock, S; Ronchetti, F; Rossi, P; Rowntree, D; Rubin, P D; Sabatié, F; Sabourov, K; Salgado, C; Sapunenko, V; Sargsyan, M; Schumacher, R A; Serov, V S; Shafi, A; Sharabian, Y G; Shaw, J; Skabelin, A V; Smith, E S; Smith, T; Smith, L C; Sober, D I; Sorrell, L; Spraker, M; Stavinsky, A; Stepanyan, S; Stoler, P; Strakovsky, I I; Taylor, S; Tedeschi, D J; Thompson, R; Todor, L; Ungaro, M; Vineyard, M F; Vlassov, A V; Wang, K; Weinstein, L B; Weisberg, A; Weygand, D P; Whisnant, C S; Wolin, E; Yegneswaran, A; Yun, J; Zhang, B; Zhao, J; Zhou, Z

2002-02-25

The double spin asymmetry in the (-->)e(-->)p --> e(prime)pi(+)n reaction has been measured for the first time in the resonance region for four-momentum transfer Q2 = 0.35-1.5 GeV(2). Data were taken at Jefferson Lab with the CLAS detector using a 2.6 GeV polarized electron beam incident on a polarized solid NH3 target. Comparison with predictions of phenomenological models shows strong sensitivity to resonance contributions. Helicity-1/2 transitions are found to be dominant in the second and third resonance regions. The measured asymmetry is consistent with a faster rise with Q(2) of the helicity asymmetry A1 for the F(15)(1680) resonance than expected from the analysis of the unpolarized data.

Direct assignment of the cysteinyl, the slowly exchangeable, and the aromatic ring H nuclear magnetic resonances in clostridial-type ferredoxins. [Clostridium acidi-urici, C. pasteurianum, C. perfringens, Peptococcus aerogenes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Packer, E.L.; Sweeney, W.V.; Rabinowitz, J.C.

1977-04-10

We have directly assigned the /sup 1/H NMR corresponding to the cysteinyl protons, the slowly exchangeable protons, and the aromatic ring protons in the /sup 1/H NMR spectrum of Clostridium acidi-urici ferredoxin by isotopic labeling and /sup 13/C NMR decoupling techniques. We also show that the resonance pattern in the 8- to 20-ppM (from 2,2-dimethyl-2-sialapentanesulfonic acid) region of the /sup 1/H NMR spectra of oxidized Clostridium acidi-urici, Clostridium pasteurianum, Clostridium perfringens, and Peptococcus aerogenes ferredoxins are very similar, and we assign the resonances in this region by analogy with the spectrum of C. acidi-urici ferredoxin. The /sup 1/H NMR spectramore » of the ..beta.. protons of the cysteinyl residues of these ferredoxins differ, however, from the /sup 1/H NMR spectra of equivalent ..beta.. protons of the methylene carbon atoms bonded via a sulfur atom to (4Fe-4S) clusters in synthetic inorganic analogues. In the spectra of the synthetic compounds, the ..beta.. protons appear as a single resonance shifted 10 ppM from its unbonded reference position. In the spectra of oxidized clostridial ferredoxins, the cysteinyl ..beta.. protons appear as a series of at least eight resolved resonances with shifts that range from 6 to 14 ppM, relative to the free amino acid resonance position.« less

A closer look at the nitrogen next door: 1H-15N NMR methods for glycosaminoglycan structural characterization

NASA Astrophysics Data System (ADS)

Langeslay, Derek J.; Beni, Szabolcs; Larive, Cynthia K.

2012-03-01

Recently, experimental conditions were presented for the detection of the N-sulfoglucosamine (GlcNS) NHSO3- or sulfamate 1H and 15N NMR resonances of the pharmaceutically and biologically important glycosaminoglycan (GAG) heparin in aqueous solution. In the present work, we explore further the applicability of nitrogen-bound proton detection to provide structural information for GAGs. Compared to the detection of 15N chemical shifts of aminosugars through long-range couplings using the IMPACT-HNMBC pulse sequence, the more sensitive two-dimensional 1H-15N HSQC-TOCSY experiments provided additional structural data. The IMPACT-HNMBC experiment remains a powerful tool as demonstrated by the spectrum measured for the unsubstituted amine of 3-O-sulfoglucosamine (GlcN(3S)), which cannot be observed with the 1H-15N HSQC-TOCSY experiment due to the fast exchange of the amino group protons with solvent. The 1H-15N HSQC-TOCSY NMR spectrum reported for the mixture of model compounds GlcNS and N-acetylglucosamine (GlcNAc) demonstrate the broad utility of this approach. Measurements for the synthetic pentasaccharide drug Arixtra® (Fondaparinux sodium) in aqueous solution illustrate the power of this NMR pulse sequence for structural characterization of highly similar N-sulfoglucosamine residues in GAG-derived oligosaccharides.

Highly repeatable room temperature negative differential resistance in AlN/GaN resonant tunneling diodes grown by molecular beam epitaxy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Growden, Tyler A.; Fakhimi, Parastou; Berger, Paul R., E-mail: pberger@ieee.org

AlN/GaN resonant tunneling diodes grown on low dislocation density semi-insulating bulk GaN substrates via plasma-assisted molecular-beam epitaxy are reported. The devices were fabricated using a six mask level, fully isolated process. Stable room temperature negative differential resistance (NDR) was observed across the entire sample. The NDR exhibited no hysteresis, background light sensitivity, or degradation of any kind after more than 1000 continuous up-and-down voltage sweeps. The sample exhibited a ∼90% yield of operational devices which routinely displayed an average peak current density of 2.7 kA/cm{sup 2} and a peak-to-valley current ratio of ≈1.15 across different sizes.

Triple Resonance Solid State NMR Experiments with Reduced Dimensionality Evolution Periods

NASA Astrophysics Data System (ADS)

Astrof, Nathan S.; Lyon, Charles E.; Griffin, Robert G.

2001-10-01

Two solid state NMR triple resonance experiments which utilize the simultaneous incrementation of two chemical shift evolution periods to obtain a spectrum with reduced dimensionality are described. The CON CA experiment establishes the correlation of 13Ci-1 to 13Cαi and 15Ni by simultaneously encoding the 13COi-1 and 15Ni chemical shifts. The CAN COCA experiment establishes the correlation 13Cai and 15COi to 13Cαi-1 and 15Ni-1 within a single experiment by simultaneous encoding of the 13Cαi and 15Ni chemical shifts. This experiment establishes sequential amino acid correlations in close analogy to the solution state HNCA experiment. Reduced dimensionality 2D experiments are a practical alternative to recording multiple 3D data sets for the purpose of obtaining sequence-specific resonance assignments of peptides and proteins in the solid state.

Cerebral glutamine metabolism under hyperammonemia determined in vivo by localized 1H and 15N NMR spectroscopy

PubMed Central

Cudalbu, Cristina; Lanz, Bernard; Duarte, João MN; Morgenthaler, Florence D; Pilloud, Yves; Mlynárik, Vladimir; Gruetter, Rolf

2012-01-01

Brain glutamine synthetase (GS) is an integral part of the glutamate–glutamine cycle and occurs in the glial compartment. In vivo Magnetic Resonance Spectroscopy (MRS) allows noninvasive measurements of the concentrations and synthesis rates of metabolites. 15N MRS is an alternative approach to 13C MRS. Incorporation of labeled 15N from ammonia in cerebral glutamine allows to measure several metabolic reactions related to nitrogen metabolism, including the glutamate–glutamine cycle. To measure 15N incorporation into the position 5N of glutamine and position 2N of glutamate and glutamine, we developed a novel 15N pulse sequence to simultaneously detect, for the first time, [5-15N]Gln and [2-15N]Gln+Glu in vivo in the rat brain. In addition, we also measured for the first time in the same experiment localized 1H spectra for a direct measurement of the net glutamine accumulation. Mathematical modeling of 1H and 15N MRS data allowed to reduce the number of assumptions and provided reliable determination of GS (0.30±0.050 μmol/g per minute), apparent neurotransmission (0.26±0.030 μmol/g per minute), glutamate dehydrogenase (0.029±0.002 μmol/g per minute), and net glutamine accumulation (0.033±0.001 μmol/g per minute). These results showed an increase of GS and net glutamine accumulation under hyperammonemia, supporting the concept of their implication in cerebral ammonia detoxification. PMID:22167234

Double cross-polarization MAS NMR in the assignment of abundant-spin resonances: ¹⁹F-{²⁹Si}-¹⁹F FBCP/MAS NMR of fluoride ions incorporated in calcium silicate hydrate (C-S-H) phases.

PubMed

Tran, Thuan T; Bildsøe, Henrik; Jakobsen, Hans J; Skibsted, Jørgen

2012-08-01

A new version of the double cross-polarization MAS NMR experiment, which transfers polarization Forth and Back (FBCP) between high- and low-γ spin nuclei, is presented. The pulse sequence is demonstrated by ¹⁹F-{²⁹Si}-¹⁹F and ¹⁹F-{¹³C}-¹⁹F FBCP NMR spectra of a mixture of cuspidine (Ca₄Si₂O₇F₂) and Teflon (-CF₂-)(n). The experiment is useful for assignment of the high-γ spin resonances, as demonstrated by ¹⁹F-{²⁹Si}-¹⁹F FBCP NMR of a fluoride-containing calcium-silicate-hydrate (C-S-H) phase, where the ¹⁹F resonance from fluoride ions incorporated in the interlayer structure of the C-S-H phase is identified. Copyright © 2012 Elsevier Inc. All rights reserved.

Optimizing Marine Security Guard Assignments

DTIC Science & Technology

2011-06-01

Bangkok, Thailand East Asia and Pacific 18 4 Fort Lauderdale, Florida Western Hemisphere - South 13 5 Frankfurt, Germany Western Europe and Scandinavia 15...Marine-billet assignment using similar fit criteria, such as rank and gender . 3. Minimize the amount of movement when filling the billets. That is, their...more than once. Gender Female MSGs will not be assigned to embassies that are not configured for females. DC Only DC-qualified MSGs are assigned to DC

Don't let the flu catch you: agency assignment in printed educational materials about the H1N1 influenza virus.

PubMed

McGlone, Matthew S; Bell, Robert A; Zaitchik, Sarah T; McGlynn, Joseph

2013-01-01

In English and in other languages, the agency for viral transmission can be grammatically assigned to people (e.g., Thousands may contract H1N1) or to the virus itself (e.g., H1N1 may infect thousands). These assignment options shape different conceptions of transmission as attributable either to social contact within one's control or to pursuit of an active predator. The authors tested the effect of agency assignment and agentic images on young adults' (N = 246) reactions to educational materials about H1N1 influenza. The authors hypothesized that assigning agency to the virus would heighten perceived severity and personal susceptibility relative to human agency assignment. Results were consistent with this hypothesis, indicating that virus agency increased perceptions of severity, personal susceptibility, and reported intentions to seek vaccination relative to human agency. The image manipulation did not directly affect these factors. The findings suggest that strategic agency assignment can improve the effectiveness of educational materials about influenza and other health threats.

Construction of 0.15 Tesla Overhauser Enhanced MRI.

PubMed

Tokunaga, Yuumi; Nakao, Motonao; Naganuma, Tatsuya; Ichikawa, Kazuhiro

2017-01-01

Overhauser enhanced MRI (OMRI) is one of the free radical imaging technologies and has been used in biomedical research such as for partial oxygen measurements in tumor, and redox status in acute oxidative diseases. The external magnetic field of OMRI is frequently in the range of 5-10 mTesla to ensure microwave penetration into small animals, and the S/N ratio is limited. In this study, a 0.15 Tesla OMRI was constructed and tested to improve the S/N ratio for a small sample, or skin measurement. Specification of the main magnet was as follows: 0.15 Tesla permanent magnet; gap size 160 mm; homogenous spherical volume of 80 mm in diameter. The OMRI resonator was designed based on TE 101 cavity mode and machined from a phosphorus deoxidized copper block for electron spin resonance (ESR) excitation and a solenoid transmission/receive resonator for NMR detection. The resonant frequencies and Q values were 6.38 MHz/150 and 4.31-4.41 GHz/120 for NMR and ESR, respectively. The Q values were comparable to those of conventional low field OMRI resonators at 15 mTesla. As expected, the MRI S/N ratio was improved by a factor of 30. Triplet dynamic nuclear polarization spectra were observed for 14 N carboxy-PROXYL, along the excitation microwave sweep. In the current setup, the enhancement factor was ca. 0.5. In conclusion, the results of this preliminary evaluation indicate that the 0.15 Tesla OMRI could be useful for free radical measurement for small samples.

N× N optical switch based on cascaded microring resonators

NASA Astrophysics Data System (ADS)

Li, Jing-sen; Lu, Huan-yu; Zhao, Yu-lin

2018-05-01

An N×N optical switch based on cascaded microring resonators on chip is proposed. As an example, the 4×4 optical switch is further investigated. It is successfully demonstrated that its insertion loss is relatively low as 2.2 dB, the crosstalk is negligible, and the extinction ratio ( ER) is as large as 130 dB. Thermal tuning is employed to make the microrings be in resonance or not, which leads to a response time of several hundred microseconds. Alternatively, doping the desired waveguide regions with p-type or n-type dopants is able to achieve a better response time of several nanoseconds. The proposed design is easily integrated to a large scale with less microring resonators, which ensures the compact size and the low power consumption.

Analysis of high-efficiency widely-tunable N-resonances in Cs vapor

NASA Astrophysics Data System (ADS)

Krasteva, A.; Gateva, S.; Tzvetkov, S.; Ghosh, P. N.; Sargsyan, A.; Cartaleva, S.

2018-03-01

The narrow-band coherent N-type resonance, promising for the development of advanced atomic clocks, can be considered as a type of three-photon resonance, where a two-photon Raman excitation is combined with a resonant optical pumping field. In this communication, we present an experimental study and a theoretical analysis related to three-photon, bi-chromatic excitation of Cs atomic vapor contained in an 8-mm long cell with 20 Torr of neon. If a coupling laser is fixed at a frequency that is lower by several GHz than the position of the absorption profile of the Fg = 4 set of transitions, and a probe laser is tuned over the D2 line (λ = 852 nm), a narrow high-contrast enhanced absorption N-resonance will be observed in the probe light profile, superimposed on the absorption profile of the Fg = 4 set of transitions. We present theoretical modeling aimed to clarify the processes behind the efficiency of the N-resonance preparation for different frequency positions of the coupling laser within the D2 line of Cs.

Resolution enhancement in 13C and 15N magic-angle turning experiments with TPPM decoupling.

PubMed

McGeorge, G; Alderman, D W; Grant, D M

1999-03-01

Many solid-state spectra have been shown to have problems related to the poor proton decoupling of carbon nuclei in methylene groups under conditions of slow magic-angle turning. Two-pulse phase-modulation (TPPM) decoupling during the 2D PHORMAT chemical shift separation experiment is shown to be more effective in comparison to that obtainable at much higher spin rates using conventional CW decoupling. TPPM decoupling can also alleviate similar inadequacies when observing the 15N nucleus, particularly with NH2 groups. This is demonstrated in the 15N resonances of fully labeled l-arginine hydrochloride, where a line narrowing of about a factor of two was observed at moderate rotation rates. This significant advantage was also obtained at turning frequencies as low as 500 Hz. Copyright 1999 Academic Press.

Vortices at the magnetic equator generated by hybrid Alfvén resonant waves

NASA Astrophysics Data System (ADS)

Hiraki, Yasutaka

2015-01-01

We performed three-dimensional magnetohydrodynamic simulations of shear Alfvén waves in a full field line system with magnetosphere-ionosphere coupling and plasma non-uniformities. Feedback instability of the Alfvén resonant modes showed various nonlinear features under the field line cavities: (i) a secondary flow shear instability occurs at the magnetic equator, (ii) trapping of the ionospheric Alfvén resonant modes facilitates deformation of field-aligned current structures, and (iii) hybrid Alfvén resonant modes grow to cause vortices and magnetic oscillations around the magnetic equator. Essential features in the initial brightening of auroral arc at substorm onsets could be explained by the dynamics of Alfvén resonant modes, which are the nature of the field line system responding to a background rapid change.

N-15 NMR Spectroscopy as a Method for Comparing the Rates of Imidization of Several Diamines

NASA Technical Reports Server (NTRS)

Johnson, J. Christopher; Kuczmarski, Maria A.

2006-01-01

The relative rates of the conversion of amide-acid to imide was measured for a series or aromatic diamines that have been identified as potential replacements for 4,4'-methylene dianiline (MDA) in high-temperature polyimides and polymer composites. These rates were compared with the N-15 NMR resonances of the unreacted amines. The initial rates of imidization track with the difference in chemical shift between the amine nitrogens in MDA and those in the subject diamines. This comparison demonstrated that N-15 NMR spectroscopy is appropriate for the rapid screening of candidate diamines to determine their reactivity relative to MDA, and can serve to provide guidance to the process of creating the time-temperature profiles used in processing these materials into polymer matrix composites.

Diabetes induced renal urea transport alterations assessed with 3D hyperpolarized 13 C,15 N-Urea.

PubMed

Bertelsen, Lotte B; Nielsen, Per M; Qi, Haiyun; Nørlinger, Thomas S; Zhang, Xiaolu; Stødkilde-Jørgensen, Hans; Laustsen, Christoffer

2017-04-01

In the current study, we investigated hyperpolarized urea as a possible imaging biomarker of the renal function by means of the intrarenal osmolality gradient. Hyperpolarized three-dimensional balanced steady state 13 C MRI experiments alongside kidney function parameters and quantitative polymerase chain reaction measurements was performed on two groups of rats, a streptozotocin type 1 diabetic group and a healthy control group. A significant decline in intrarenal steepness of the urea gradient was found after 4 weeks of untreated insulinopenic diabetes in agreement with an increased urea transport transcription. MRI and hyperpolarized [ 13 C, 15 N]urea can monitor the changes in the corticomedullary urea concentration gradients in diabetic and healthy control rats. Magn Reson Med 77:1650-1655, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

15N photo-CIDNP MAS NMR analysis of reaction centers of Chloracidobacterium thermophilum.

PubMed

Zill, Jeremias C; He, Zhihui; Tank, Marcus; Ferlez, Bryan H; Canniffe, Daniel P; Lahav, Yigal; Bellstedt, Peter; Alia, A; Schapiro, Igor; Golbeck, John H; Bryant, Donald A; Matysik, Jörg

2018-03-30

Photochemically induced dynamic nuclear polarization (photo-CIDNP) has been observed in the homodimeric, type-1 photochemical reaction centers (RCs) of the acidobacterium, Chloracidobacterium (Cab.) thermophilum, by 15 N magic-angle spinning (MAS) solid-state NMR under continuous white-light illumination. Three light-induced emissive (negative) signals are detected. In the RCs of Cab. thermophilum, three types of (bacterio)chlorophylls have previously been identified: bacteriochlorophyll a (BChl a), chlorophyll a (Chl a), and Zn-bacteriochlorophyll a' (Zn-BChl a') (Tsukatani et al. in J Biol Chem 287:5720-5732, 2012). Based upon experimental and quantum chemical 15 N NMR data, we assign the observed signals to a Chl a cofactor. We exclude Zn-BChl because of its measured spectroscopic properties. We conclude that Chl a is the primary electron acceptor, which implies that the primary donor is most likely Zn-BChl a'. Chl a and 8 1 -OH Chl a have been shown to be the primary electron acceptors in green sulfur bacteria and heliobacteria, respectively, and thus a Chl a molecule serves this role in all known homodimeric type-1 RCs.

GaN Micromechanical Resonators with Meshed Metal Bottom Electrode.

PubMed

Ansari, Azadeh; Liu, Che-Yu; Lin, Chien-Chung; Kuo, Hao-Chung; Ku, Pei-Cheng; Rais-Zadeh, Mina

2015-03-17

This work describes a novel architecture to realize high-performance gallium nitride (GaN) bulk acoustic wave (BAW) resonators. The method is based on the growth of a thick GaN layer on a metal electrode grid. The fabrication process starts with the growth of a thin GaN buffer layer on a Si (111) substrate. The GaN buffer layer is patterned and trenches are made and refilled with sputtered tungsten (W)/silicon dioxide (SiO₂) forming passivated metal electrode grids. GaN is then regrown, nucleating from the exposed GaN seed layer and coalescing to form a thick GaN device layer. A metal electrode can be deposited and patterned on top of the GaN layer. This method enables vertical piezoelectric actuation of the GaN layer using its largest piezoelectric coefficient ( d 33 ) for thickness-mode resonance. Having a bottom electrode also results in a higher coupling coefficient, useful for the implementation of acoustic filters. Growth of GaN on Si enables releasing the device from the frontside using isotropic xenon difluoride (XeF₂) etch and therefore eliminating the need for backside lithography and etching.

Ultra-high magnetic resonance imaging (MRI): a potential examination for deep brain stimulation devices and the limitation study concerning MRI-related heating injury.

PubMed

Chen, Ying-Chuan; Li, Jun-Ju; Zhu, Guan-Yu; Shi, Lin; Yang, An-Chao; Jiang, Yin; Zhang, Xin; Zhang, Jian-Guo

2017-03-01

Nowadays, the patients with deep brain stimulation (DBS) devices are restricted to undertake 1.5T magnetic resonance imaging (MRI) according to the guideline. Nevertheless, we conducted an experiment to test pathological change near the leads in different field-strength MRI. Twenty-four male New Zealand rabbits were assigned to Group 1 (G1, n = 6, 7.0T, DBS), Group 2 (G2, n = 6, 3.0T, DBS), Group 3 (G3, n = 6, 1.5T, DBS), and Group 4 (G4, n = 6, 1.5T, paracentesis). DBS leads were implanted in G1, G2 and G3, targeting left nucleus ventralis posterior thalami. Paracentesis was performed in G4. 24 h after MRI scan, all animals were killed for examining pathological alternation (at different distance from lead) via transmission electron microscopy. Our results suggest that the severity of tissue injury correlates with the distance to electrode instead of field strength of MRI. Up to now, the reason for the restriction of MRI indicated no significantly different pathological change.

Backbone resonance assignments for G protein α(i3) subunit in the GDP-bound state.

PubMed

Mase, Yoko; Yokogawa, Mariko; Osawa, Masanori; Shimada, Ichio

2014-10-01

Guanine-nucleotide binding proteins (G proteins) serve as molecular switches in signaling pathways, by coupling the activation of G protein-coupled receptors (GPCRs) at the cell surface to intracellular responses. In the resting state, G protein forms a heterotrimer, consisting of the G protein α subunit with GDP (Gα·GDP) and the G protein βγ subunit (Gβγ). Ligand binding to GPCRs promotes the GDP-GTP exchange on Gα, leading to the dissociation of the GTP-bound form of Gα (Gα·GTP) and Gβγ. Then, Gα·GTP and Gβγ bind to their downstream effector enzymes or ion channels and regulate their activities, leading to a variety of cellular responses. Finally, Gα hydrolyzes the bound GTP to GDP and returns to the resting state by re-associating with Gβγ. The G proteins are classified with four major families based on the amino acid sequences of Gα: i/o, s, q/11, and 12/13. Here, we established the backbone resonance assignments of human Gαi3, a member of the i/o family with a molecular weight of 41 K, in complex with GDP. The chemical shifts were compared with those of Gα(i3) in complex with a GTP-analogue, GTPγS, which we recently reported, indicating that the residues with significant chemical shift differences are mostly consistent with the regions with the structural differences between the GDP- and GTPγS-bound states, as indicated in the crystal structures. The assignments of Gα(i3)·GDP would be useful for the analyses of the dynamics of Gα(i3) and its interactions with various target molecules.

Ultrafast Independent N-H and N-C Bond Deformation Investigated with Resonant Inelastic X-Ray Scattering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eckert, Sebastian; Norell, Jesper; Miedema, Piter S.

Here, the femtosecond excited-state dynamics following resonant photoexcitation enable the selective deformation of N-H and N-C chemical bonds in 2-thiopyridone in aqueous solution with optical or X-ray pulses. In combination with multiconfigurational quantum-chemical calculations, the orbital-specific electronic structure and its ultrafast dynamics accessed with resonant inelastic X-ray scattering at the N 1s level using synchrotron radiation and the soft X-ray free-electron laser LCLS provide direct evidence for this controlled photoinduced molecular deformation and its ultrashort timescale.

Ultrafast Independent N-H and N-C Bond Deformation Investigated with Resonant Inelastic X-Ray Scattering

DOE PAGES

Eckert, Sebastian; Norell, Jesper; Miedema, Piter S.; ...

2017-04-04

Here, the femtosecond excited-state dynamics following resonant photoexcitation enable the selective deformation of N-H and N-C chemical bonds in 2-thiopyridone in aqueous solution with optical or X-ray pulses. In combination with multiconfigurational quantum-chemical calculations, the orbital-specific electronic structure and its ultrafast dynamics accessed with resonant inelastic X-ray scattering at the N 1s level using synchrotron radiation and the soft X-ray free-electron laser LCLS provide direct evidence for this controlled photoinduced molecular deformation and its ultrashort timescale.

High Resolution 13C MRI With Hyperpolarized Urea: In Vivo T2 Mapping and 15N Labeling Effects

PubMed Central

Reed, Galen D.; von Morze, Cornelius; Bok, Robert; Koelsch, Bertram L.; Van Criekinge, Mark; Smith, Kenneth J.; Shang, Hong; Larson, Peder E. Z.; Kurhanewicz, John; Vigneron, Daniel B.

2014-01-01

13C steady state free precession (SSFP) magnetic resonance imaging and effective spin-spin relaxation time (T2) mapping were performed using hyperpolarized [13C] urea and [13C, 15N2] urea injected intravenously in rats. 15N labeling gave large T2 increases both in solution and in vivo due to the elimination of a strong scalar relaxation pathway. The T2 increase was pronounced in the kidney, with [13C, 15N2] urea giving T2 values of 6.3±1.3 s in the cortex and medulla, and 11±2 s in the renal pelvis. The measured T2 in the aorta was 1.3±0.3 s. [13C] urea showed shortened T2 values in the kidney of 0.23±0.03 s compared to 0.28±0.03 s measured in the aorta. The enhanced T2 of [13C, 15N2] urea was utilized to generate large signal enhancement by SSFP acquisitions with flip angles approaching the fully refocused regime. Projection images at 0.94 mm in-plane resolution were acquired with both urea isotopes, with [13C, 15N2] urea giving a greater than four-fold increase in signal-to-noise ratio [13C] over urea. PMID:24235273

15N-labeled glycine synthesis.

PubMed

Tavares, Claudinéia R O; Bendassolli, José A; Coelho, Fernando; Sant'ana Filho, Carlos R; Prestes, Clelber V

2006-09-01

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 important tool for N cycling studies in living organisms, also minimizing labor and environmental hazards, as well as time limitation problems in field studies. The tests were carried out with three replications, and variable 15NH3aq volumes in the reaction were used (50, 100, and 150 mL), in order to calibrate the best operational condition; glycine masses obtained were 1.7, 2, and 3.2 g, respectively. With the development of a system for 15NH3 recovery, it was possible to recover 71, 83, and 87% of the ammonia initially used in the synthesis. With the required adaptations, the same system was used to recover methanol, and 75% of the methanol initially used in the amino acid purification process were recovered.

Millimeter-wave optical double resonance schemes for rapid assignment of perturbed spectra, with applications to the C{sup ~} {sup 1}B{sub 2} state of SO{sub 2}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, G. Barratt, E-mail: barratt@mit.edu, E-mail: barratt.park@gmail.com; Womack, Caroline C.; Jiang, Jun

2015-04-14

Millimeter-wave detected, millimeter-wave optical double resonance (mmODR) spectroscopy is a powerful tool for the analysis of dense, complicated regions in the optical spectra of small molecules. The availability of cavity-free microwave and millimeter wave spectrometers with frequency-agile generation and detection of radiation (required for chirped-pulse Fourier-transform spectroscopy) opens up new schemes for double resonance experiments. We demonstrate a multiplexed population labeling scheme for rapid acquisition of double resonance spectra, probing multiple rotational transitions simultaneously. We also demonstrate a millimeter-wave implementation of the coherence-converted population transfer scheme for background-free mmODR, which provides a ∼10-fold sensitivity improvement over the population labeling scheme.more » We analyze perturbations in the C{sup ~} state of SO{sub 2}, and we rotationally assign a b{sub 2} vibrational level at 45 328 cm{sup −1} that borrows intensity via a c-axis Coriolis interaction. We also demonstrate the effectiveness of our multiplexed mmODR scheme for rapid acquisition and assignment of three predissociated vibrational levels of the C{sup ~} state of SO{sub 2} between 46 800 and 47 650 cm{sup −1}.« less

NMR assignments of SPOC domain of the human transcriptional corepressor SHARP in complex with a C-terminal SMRT peptide.

PubMed

Mikami, Suzuka; Kanaba, Teppei; Ito, Yutaka; Mishima, Masaki

2013-10-01

The transcriptional corepressor SMRT/HDAC1-associated repressor protein (SHARP) recruits histone deacetylases. Human SHARP protein is thought to function in processes involving steroid hormone responses and the Notch signaling pathway. SHARP consists of RNA recognition motifs (RRMs) in the N-terminal region and the spen paralog and ortholog C-terminal (SPOC) domain in the C-terminal region. It is known that the SPOC domain binds the LSD motif in the C-terminal tail of corepressors silencing mediator for retinoid and thyroid receptor (SMRT)/nuclear receptor corepressor (NcoR). We are interested in delineating the mechanism by which the SPOC domain recognizes the LSD motif of the C-terminal tail of SMRT/NcoR. To this end, we are investigating the tertiary structure of the SPOC/SMRT peptide using NMR. Herein, we report on the (1)H, (13)C and (15)N resonance assignments of the SPOC domain in complex with a SMRT peptide, which contributes towards a structural understanding of the SPOC/SMRT peptide and its molecular recognition.

The EIT- and N- joint resonance lineshape asymmetry

NASA Astrophysics Data System (ADS)

Crescimanno, Michael; Hancox, Cindy; Hohensee, Michael; Phillips, David; Walsworth, Ron

2008-03-01

The solution of a quantum optics model for the joint EIT- and N- resonance explains the experimentally observed two-photon lineshape asymmetry as arising from interference and AC stark effects. This solution is evaluated for various light field intensities, detunings and couplings associated with experiments performed on the D1 and D2 transition of 87Rb. Because of its contribution to clock instability, lineshape asymmetry remains perhaps the main impediment to improving all-optical time standards based on the joint resonance.

Combination of liquid chromatography-Fourier transform ion cyclotron resonance-mass spectrometry with 13C-labeling for chemical assignment of sulfur-containing metabolites in onion bulbs.

PubMed

Nakabayashi, Ryo; Sawada, Yuji; Yamada, Yutaka; Suzuki, Makoto; Hirai, Masami Yokota; Sakurai, Tetsuya; Saito, Kazuki

2013-02-05

Phytochemicals containing heteroatoms (N, O, S, and halogens) often have biological activities that are beneficial to humans. Although targeted profiling methods for such phytochemicals are expected to contribute to rapid chemical assignments, thus making phytochemical genomics and crop breeding much more efficient, there are few profiling methods for the metabolites. Here, as an ultrahigh performance approach, we propose a practical profiling method for S-containing metabolites (S-omics) using onions (Allium cepa) as a representative species and (12)C- and (13)C-based mass spectrometry (MS) and tandem mass spectrometry (MS/MS) analyses by liquid chromatography-Fourier transform ion cyclotron resonance-mass spectrometry (LC-FTICR-MS). Use of the ultrahigh quality data from FTICR-MS enabled simplifying the previous methods to determine specific elemental compositions. MS analysis with a resolution of >250,000 full width at half-maximum and a mass accuracy of <1 ppm can distinguish S-containing monoisotopic ions from other ions on the basis of the natural abundance of (32)S and (34)S and the mass differences among the S isotopes. Comprehensive peak picking using the theoretical mass difference (1.99579 Da) between (32)S-containing monoisotopic ions and their (34)S-substituted counterparts led to the assignment of 67 S-containing monoisotopic ions from the (12)C-based MS spectra, which contained 4693 chromatographic ions. The unambiguous elemental composition of 22 ions was identified through comparative analysis of the (12)C- and (13)C-based MS spectra. Finally, of these, six ions were found to be derived from S-alk(en)ylcysteine sulfoxides and glutathione derivatives. This S-atom-driven approach afforded an efficient chemical assignment of S-containing metabolites, suggesting its potential application for screening not only S but also other heteroatom-containing metabolites in MS-based metabolomics.

HN(α/β-COCA-J) Experiment for Measurement of 1JC‧Cα Couplings from Two-Dimensional [15N, 1H] Correlation Spectrum

NASA Astrophysics Data System (ADS)

Permi, Perttu; Sorsa, Tia; Kilpeläinen, Ilkka; Annila, Arto

1999-11-01

Anew method for measurement of one-bond 13C‧-13Cα scalar and dipolar couplings from a two-dimensional [15N, 1H] correlation spectrum is presented. The experiment is based on multiple-quantum coherence, which is created between nitrogen and carbonyl carbon for simultaneous evolution of 15N chemical shift and coupling between 13C‧ and 13Cα. Optional subspectral editing is provided by the spin-state-selective filters. The residual dipolar dipolar contribution to the 13C‧-13Cα coupling can be measured from these simplified [15N, 1H]-HSQC-like spectra. In this way, without explicit knowledge of carbon assignments, conformational changes of proteins dissolved in dilute liquid crystals can be probed conveniently, e.g., in structure activity relationship by NMR studies. The method is demonstrated with human cardiac troponin C.

Theoretical study of platonic crystals with periodically structured N-beam resonators

NASA Astrophysics Data System (ADS)

Gao, Penglin; Climente, Alfonso; Sánchez-Dehesa, José; Wu, Linzhi

2018-03-01

A multiple scattering theory is applied to study the properties of flexural waves propagating in a plate with periodically structured N-beam resonators. Each resonator consists of a circular hole containing an inner disk connected to background plate with N rectangular beams. The Bloch theorem is employed to obtain the band structure of a two-dimensional lattice containing a single resonator per unit cell. Also, a numerical algorithm has been developed to get the transmittance through resonator slabs infinitely long in the direction perpendicular to the incident wave. For the numerical validation, a square lattice of 2-beam resonators has been comprehensively analyzed. Its band structure exhibits several flat bands, indicating the existence of local resonances embedded in the structure. Particularly, the one featured as the fundamental mode of the inner disk opens a bandgap at low frequencies. This mode has been fully described in terms of a simple spring-mass model. As a practical application of the results obtained, a homogenization approach has been employed to design a focusing lens for flexural waves, where the index gradient is obtained by adjusting the orientation of the resonators beams. Numerical experiments performed within the framework of a three-dimensional finite element method have been employed to discuss the accuracy of the models described here.

Combining multinuclear high-resolution solid-state MAS NMR and computational methods for resonance assignment of glutathione tripeptide.

PubMed

Sardo, Mariana; Siegel, Renée; Santos, Sérgio M; Rocha, João; Gomes, José R B; Mafra, Luis

2012-06-28

We present a complete set of experimental approaches for the NMR assignment of powdered tripeptide glutathione at natural isotopic abundance, based on J-coupling and dipolar NMR techniques combined with (1)H CRAMPS decoupling. To fully assign the spectra, two-dimensional (2D) high-resolution methods, such as (1)H-(13)C INEPT-HSQC/PRESTO heteronuclear correlations (HETCOR), (1)H-(1)H double-quantum (DQ), and (1)H-(14)N D-HMQC correlation experiments, have been used. To support the interpretation of the experimental data, periodic density functional theory calculations together with the GIPAW approach have been used to calculate the (1)H and (13)C chemical shifts. It is found that the shifts calculated with two popular plane wave codes (CASTEP and Quantum ESPRESSO) are in excellent agreement with the experimental results.

NVR-BIP: Nuclear Vector Replacement using Binary Integer Programming for NMR Structure-Based Assignments.

PubMed

Apaydin, Mehmet Serkan; Çatay, Bülent; Patrick, Nicholas; Donald, Bruce R

2011-05-01

Nuclear magnetic resonance (NMR) spectroscopy is an important experimental technique that allows one to study protein structure and dynamics in solution. An important bottleneck in NMR protein structure determination is the assignment of NMR peaks to the corresponding nuclei. Structure-based assignment (SBA) aims to solve this problem with the help of a template protein which is homologous to the target and has applications in the study of structure-activity relationship, protein-protein and protein-ligand interactions. We formulate SBA as a linear assignment problem with additional nuclear overhauser effect constraints, which can be solved within nuclear vector replacement's (NVR) framework (Langmead, C., Yan, A., Lilien, R., Wang, L. and Donald, B. (2003) A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments. Proc. the 7th Annual Int. Conf. Research in Computational Molecular Biology (RECOMB) , Berlin, Germany, April 10-13, pp. 176-187. ACM Press, New York, NY. J. Comp. Bio. , (2004), 11, pp. 277-298; Langmead, C. and Donald, B. (2004) An expectation/maximization nuclear vector replacement algorithm for automated NMR resonance assignments. J. Biomol. NMR , 29, 111-138). Our approach uses NVR's scoring function and data types and also gives the option of using CH and NH residual dipolar coupling (RDCs), instead of NH RDCs which NVR requires. We test our technique on NVR's data set as well as on four new proteins. Our results are comparable to NVR's assignment accuracy on NVR's test set, but higher on novel proteins. Our approach allows partial assignments. It is also complete and can return the optimum as well as near-optimum assignments. Furthermore, it allows us to analyze the information content of each data type and is easily extendable to accept new forms of input data, such as additional RDCs.

Synthesis and biosynthesis of {sup 13}C-, {sup 15}N-labeled deoxynucleosides useful for biomolecular structural determinations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ashburn, D.A.; Garcia, K.; Hanners, J.L.

Currently, there is a great emphasis on elucidating the structure, function, and dynamics of DNA. Much of the research involved in this study uses nuclear magnetic resonance (NMR) spectroscopy. Effective use of NMR spectroscopy for DNA molecules with mw > 10,000 requires stable isotope enrichment. We present strategies for site-specific isotopic labeling of the purine bases adenosine and guanosine and the biosynthesis of (U-{sup 13}C, {sup 15}N) DNA from methylotropic bacteria. With commercially available 6-chloropurine, an effective two-step route leads to 2{prime}-deoxy-(amino-{sup 15}N)adenosine (dA). The resulting d(amino-{sup 15}N)A is used in a series of reactions to synthesize 2{prime}-deoxy-(2-{sup 13}C,1,amino-{sup 15}N{submore » 2})guanosine or any combination thereof. An improved biosynthesis of labeled DNA has been accomplished using Methylobacterium extorquens AS1. Each liter of growth medium contains 4 g of methanol to yield 1 g of lyophilized cells. As much as 200 mg of RNA per liter of culture has been obtained. We are currently developing large-scale isolation protocols. General synthetic pathways to oligomeric DNA will be presented.« less

X-ray Crystallographic, Multifrequency Electron Paramagnetic Resonance, and Density Functional Theory Characterization of the Ni(P(Cy)2N(tBu)2)2(n+) Hydrogen Oxidation Catalyst in the Ni(I) Oxidation State.

PubMed

Niklas, Jens; Westwood, Mark; Mardis, Kristy L; Brown, Tiara L; Pitts-McCoy, Anthony M; Hopkins, Michael D; Poluektov, Oleg G

2015-07-06

The Ni(I) hydrogen oxidation catalyst [Ni(P(Cy)2N(tBu)2)2](+) (1(+); P(Cy)2N(tBu)2 = 1,5-di(tert-butyl)-3,7-dicyclohexyl-1,5-diaza-3,7-diphosphacyclooctane) has been studied using a combination of electron paramagnetic resonance (EPR) techniques (X-, Q-, and D-band, electron-nuclear double resonance, hyperfine sublevel correlation spectroscopy), X-ray crystallography, and density functional theory (DFT) calculations. Crystallographic and DFT studies indicate that the molecular structure of 1(+) is highly symmetrical. EPR spectroscopy has allowed determination of the electronic g tensor and the spin density distribution on the ligands, and revealed that the Ni(I) center does not interact strongly with the potentially coordinating solvents acetonitrile and butyronitrile. The EPR spectra and magnetic parameters of 1(+) are found to be distinctly different from those for the related compound [Ni(P(Ph)2N(Ph)2)2](+) (4(+)). One significant contributor to these differences is that the molecular structure of 4(+) is unsymmetrical, unlike that of 1(+). DFT calculations on derivatives in which the R and R' groups are systematically varied have allowed elucidation of structure/substituent relationships and their corresponding influence on the magnetic resonance parameters.

Resonance Raman spectroscopy of 2H-labelled spheroidenes in petroleum ether and in the Rhodobacter sphaeroides reaction centre.

PubMed

Kok, P; Köhler, J; Groenen, E J; Gebhard, R; van der Hoef, I; Lugtenburg, J; Farhoosh, R; Frank, H A

1997-03-01

As a step towards the structural analysis of the carotenoid spheroidene in the Rhodobacter sphaeroides reaction centre, we present the resonance Raman spectra of 14-2H, 15-2H, 15'-2H, 14'-2H, 14,15'-2H2 and 15-15'-2H2 spheroidenes in petroleum ether and, except for 14,15'-2H2 spheroidene, in the Rb. sphaeroides R26 reaction center (RC). Analysis of the spectral changes upon isotopic substitution allows a qualitative assignment of most of the vibrational bands to be made. For the all-trans spheroidenes in solution the resonance enhancement of the Raman bands is determined by the participation of carbon carbon stretching modes in the centre of the conjugated chain, the C9 to C15' region. For the RC-bound 15,15'-cis spheroidenes, enhancement is determined by the participation of carbon-carbon stretching modes in the centre of the molecule, the C13 to C13' region. Comparison of the spectra in solution and in the RC reveals evidence for an out-of-plane distortion of the RC-bound spheroidene in the central C14 to C14' region of the carotenoid. The characteristic 1240 cm-1 band in the spectrum of the RC-bound spheroidene has been assigned to a normal mode that contains the coupled C12-C13 and C13'-C12' stretch vibrations.

The breakout of the Hot CNO cycle via ^18Ne resonant states

NASA Astrophysics Data System (ADS)

Almaraz-Calderon, S.; Tan, W.; Aprahamian, A.; Bucher, B.; Gorres, J.; Roberts, A.; Villano, A.; Wiescher, M.; Brune, C.; Heinen, Z.; Massey, T.; Ozkan, N.; Guray, R. T.; Mach, H.

2010-11-01

The energy generation rate in the HCNO cycle is limited by the β decay of the waiting point nuclei ^14O and ^15O. However, when the temperatures and densities are high enough (e.g. Novae and X-ray Bursts) it is possible to bypass them by p/α captures resulting in a thermonuclear runaway towards the rp-process. One of the two paths for breakouts from the HCNO cycle is the reaction chain ^14O(α,p)^17F(p,γ)^18Ne(α,p), which proceeds through resonant states on ^18Ne, making their reactions rates very sensitive on the partial and total widths, excitation energies and spins of such resonances. We studied the resonant states in ^18Ne via ^16O(^3He,n) reaction. The neutrons were measured with an array of liquid scintillators using Time-of-Flight and pulse-shape discrimination techniques. The charged particles were detected in coincidence with neutrons by an array of silicon detectors, allowing us to measure α, p, p' and 2p decay branching ratios. Tentative spin assignments were made in comparison with zero range DWBA calculations. This new information will be included in reaction network calculations to evaluate its impact on the nuclear energy generation that occurs in these stellar explosive environments.

15N fractionation in infrared-dark cloud cores

NASA Astrophysics Data System (ADS)

Zeng, S.; Jiménez-Serra, I.; Cosentino, G.; Viti, S.; Barnes, A. T.; Henshaw, J. D.; Caselli, P.; Fontani, F.; Hily-Blant, P.

2017-07-01

Context. Nitrogen is one of the most abundant elements in the Universe and its 14N/15N isotopic ratio has the potential to provide information about the initial environment in which our Sun formed. Recent findings suggest that the solar system may have formed in a massive cluster since the presence of short-lived radioisotopes in meteorites can only be explained by the influence of a supernova. Aims: We seek to determine the 14N/15N ratio towards a sample of cold and dense cores at the initial stages in their evolution. Methods: We observed the J = 1 → 0 transitions of HCN, H13CN, HC15N, HN13C, and H15NC towards a sample of 22 cores in four infrared-dark clouds (IRDCs) which are believed to be the precursors of high-mass stars and star clusters. Assuming LTE and a temperature of 15 K, the column densities of HCN, H13CN, HC15N, HN13C, and H15NC are calculated and their 14N/15N ratio is determined for each core. Results: The 14N/15N ratios measured in our sample of IRDC cores range between 70 and ≥763 in HCN and between 161 and 541 in HNC. These ratios are consistent with the terrestrial atmosphere (TA) and protosolar nebula (PSN) values, and with the ratios measured in low-mass prestellar cores. However, the 14N/15N ratios measured in cores C1, C3, F1, F2, and G2 do not agree with the results from similar studies towards the same cores using nitrogen bearing molecules with nitrile functional group (-CN) and nitrogen hydrides (-NH) although the ratio spread covers a similar range. Conclusions: Relatively low 14N/15N ratios amongst the four-IRDCs were measured in IRDC G which are comparable to those measured in small cosmomaterials and protoplanetary disks. The low average gas density of this cloud suggests that the gas density, rather than the gas temperature, may be the dominant parameter influencing the initial nitrogen isotopic composition in young PSN. The reduced spectra (FITS files) are only available at the CDS via anonymous ftp to http

(n,{gamma}) Experiments on tin isotopes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baramsai, B.; Mitchell, G. E.; Walker, C. L.

2013-04-19

Neutron capture experiments on highly enriched {sup 117,119}Sn isotopes were performed with the DANCE detector array located at the Los Alamos Neutron Science Center. The DANCE detector provides detailed information about the multi-step {gamma}-ray cascade following neutron capture. Analysis of the experimental data provides important information to improve understanding of the neutron capture reaction, including a test of the statistical model, the assignment of spins and parities of neutron resonances, and information concerning the Photon Strength Function (PSF) and Level Density (LD) below the neutron separation energy. Preliminary results for the (n,{gamma}) reaction on {sup 117,119}Sn are presented. Resonance spinsmore » of the odd-A tin isotopes were almost completely unknown. Resonance spins and parities have been assigned via analysis of the multi-step {gamma}-ray spectra and directional correlations.« less

¹H, ¹³C, ¹⁵N and ³¹P chemical shift assignments of a human Xist RNA A-repeat tetraloop hairpin essential for X-chromosome inactivation.

PubMed

Duszczyk, Malgorzata M; Sattler, Michael

2012-04-01

Initiation of X-chromosome inactivation in female mammals depends on the non-coding RNA Xist. We have solved the NMR structure of a 14-nucleotide hairpin with a novel AUCG tetraloop fold from a Xist A-repeat that is essential for silencing. The (1)H, (13)C, (15)N and (31)P chemical shift assignments are reported.

Proton-Detected 15N NMR-Spectroscopy and Imaging

NASA Astrophysics Data System (ADS)

Freeman, D.; Sailasuta, N.; Sukumar, S.; Hurd, R. E.

1993-10-01

Proton detection of nitrogen-15, using gradients for coherence selection, was determined to be an effective method for obtaining spectra of 15N-labeled metabolites from extracts and biopsies of tissue infused with [15N] ammonium chloride. The advantage of gradient selection of coherence was best demonstrated by the almost complete single-shot elimination of solvent water in extracts and tissue water in biopsies. As a single-acquisition editing method in which only protons attached to 15N are detected, the potential limitations of dynamic range and motion are also reduced. Gradient-enhanced heteronuclear multiple-quantum coherence (1H[15N] HMQC) was compared with conventional HMQC, and despite selection of only one of the two heteronuclear pathways, GE-HMQC was found to be more effective for resolving the desired signal for dilute solutions; and with a single scan. In addition, effective water elimination made it possible to use the resolution advantage of a frequency-encoding dimension in proton-detected 15N imaging experiments. The limit of detection of the method at 500 MHz was 0.7 mM in 16 scans from a total volume of 400 μl. Signals from tissue extracts were observable in less than one minute for kidney, heart, brain, and muscle. Proton-detected 15N GE-HMQC images with a voxel size of 39 × 78 × 625 μm were obtained at 600 MHz from a 4 mM (1.6 μmol) 15N urea sample in less than four hours. Distribution of [15N] urea in the kidney was observed in a 600 MHz GE-HMQC image of the papilla and some cortical structures.

Estimate of production of gaseous nitrogen in the human body based on (15)N analysis of breath N2 after administration of [(15)N2]urea.

PubMed

Junghans, Peter

2013-01-01

After oral administration of [(15)N2]urea (1.5 mmol, 95 atom% (15)N), we found that breath N2 was significantly (15)N-labelled. The result suggests that molecular nitrogen in breath must be partly produced endogenously. Based on a metabolic model, the endogenous N2 production was estimated to be 0.40±0.25 mmol kg(-1) d(-1) or 2.9±1.8 % of the total (urinary and faecal) N excretion in fasted healthy subjects (n=4). In patients infected with Helicobacter pylori (n=5), the endogenous N2 production was increased to 1.24±0.59 mmol kg(-1) d(-1) or 9.0±4.3 % of the total N excretion compared to the healthy controls (p<0.05). We conclude that N balance and gas exchange measurements may be affected by endogenously produced nitrogen, especially in metabolic situations with elevated nitrosation, for instance in oxidative and nitrosative stress-related diseases such as H. pylori infections.

Formularity: Software for Automated Formula Assignment of Natural and Other Organic Matter from Ultrahigh-Resolution Mass Spectra.

PubMed

Tolić, Nikola; Liu, Yina; Liyu, Andrey; Shen, Yufeng; Tfaily, Malak M; Kujawinski, Elizabeth B; Longnecker, Krista; Kuo, Li-Jung; Robinson, Errol W; Paša-Tolić, Ljiljana; Hess, Nancy J

2017-12-05

Ultrahigh resolution mass spectrometry, such as Fourier transform ion cyclotron resonance mass spectrometry (FT ICR MS), can resolve thousands of molecular ions in complex organic matrices. A Compound Identification Algorithm (CIA) was previously developed for automated elemental formula assignment for natural organic matter (NOM). In this work, we describe software Formularity with a user-friendly interface for CIA function and newly developed search function Isotopic Pattern Algorithm (IPA). While CIA assigns elemental formulas for compounds containing C, H, O, N, S, and P, IPA is capable of assigning formulas for compounds containing other elements. We used halogenated organic compounds (HOC), a chemical class that is ubiquitous in nature as well as anthropogenic systems, as an example to demonstrate the capability of Formularity with IPA. A HOC standard mix was used to evaluate the identification confidence of IPA. Tap water and HOC spike in Suwannee River NOM were used to assess HOC identification in complex environmental samples. Strategies for reconciliation of CIA and IPA assignments were discussed. Software and sample databases with documentation are freely available.

Suppressing the crosstalk between racetrack resonators by grating assisted couplers for WDM sensing

NASA Astrophysics Data System (ADS)

Zhang, Xuezhi; Jiang, Junfeng; Liu, Kun; Yu, Zhe; Feng, Ming; Chen, Wenjie; Liu, Tiegen

2017-12-01

We proposed a uniform racetrack resonators based sensor for bio-chemical WDM sensing. The sensing channels are assigned by grating assisted contra-directional couplers. Each resonator only occupies one sensing channel. The crosstalk between sensing channels can be suppressed by aligning the center coupling wavelength of one resonator with the weak coupling wavelength of the others. Based on the simulation results obtained from transfer matrix method, the sensing channel gap can be reduced down to 2 FSRs (˜1.5 nm) of the resonator. The total crosstalk can be as low as 2.5 × 10-2 dB in a sensor with 23 channels covering the whole C band. This sensor with high throughput will be very important for analyzing a wide range of analytes, such as organic compounds or biological materials.

15N Abundance of Nodules as an Indicator of N Metabolism in N2-Fixing Plants 1

PubMed Central

Shearer, Georgia; Feldman, Lori; Bryan, Barbara A.; Skeeters, Jerri L.; Kohl, Daniel H.; Amarger, Nöelle; Mariotti, Françoise; Mariotti, André

1982-01-01

This paper expands upon previous reports of 15N elevation in nodules (compared to other tissues) of N2-fixing plants. N2-Fixing nodules of Glycine max (soybeans), Vigna unguiculata (cowpea), Phaseolus vulgaris (common bean), Phaseolus coccineus (scarlet runner bean), Prosopis glandulosa (mesquite), and Olneya tesota (desert ironwood) were enriched in 15N. Nodules of Vicia faba (fava beans), Arachis hypogaea (peanut), Trifolium pratense (red clover), Pisum sativum (pea), Lathyrus sativus (grass pea), Medicago sativa (alfalfa), and Lupinus mutabilis (South American lupine) were not; nor were the nodules of nine species of N2-fixing nonlegumes. The nitrogen of ineffective nodules of soybeans and cowpeas was not enriched in 15N. Thus, 15N elevation in nodules of these plants depends on active N2-fixation. Results obtained so far on the generality of 15N enrichment in N2-fixing nodules suggest that only the nodules of plants which actively fix N2 and which transport allantoin or allantoic acid exhibit 15N enrichment. PMID:16662517

The {sup 17}F(p,{gamma}){sup 18}Ne3{sup +} resonance state studied with the {sup 16}O({sup 3}He,n){sup 18}Ne reaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parpottas, Y.; Grimes, S.M.; Brune, C.R.

2005-08-01

The astrophysically important 3{sup +} resonance of the {sup 17}F(p,{gamma}){sup 18}Ne reaction has been studied with the {sup 16}O({sup 3}He,n){sup 18}Ne reaction. High-resolution measurements were carried out for three different kinematic configurations. We find an excitation energy of 4527(4) keV and a proton width of 17(4) keV for the 3{sup +} state. Measured differential cross sections were compared with Hauser-Feshbach predictions to assign the spin of the 4527-keV state and confirm the spin assignments of the two known levels in this region. Our results differ from the earlier {sup 16}O({sup 3}He,n){sup 18}Ne findings of Garcia et al. [Phys. Rev. Cmore » 43, 2012 (1991)], but they agree well with the {sup 17}F(p,p){sup 17}F measurements of Bardayan et al. [Phys. Rev. C 62, 055804 (2002)].« less

The {sup 14}N(p,{gamma}){sup 15}O reaction studied with a composite germanium detector

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marta, M.; Bemmerer, D.; Formicola, A.

2011-04-15

The rate of the carbon-nitrogen-oxygen (CNO) cycle of hydrogen burning is controlled by the {sup 14}N(p,{gamma}){sup 15}O reaction. The reaction proceeds by capture to the ground states and several excited states in {sup 15}O. In order to obtain a reliable extrapolation of the excitation curve to astrophysical energy, fits in the R-matrix framework are needed. In an energy range that sensitively tests such fits, new cross-section data are reported here for the four major transitions in the {sup 14}N(p,{gamma}){sup 15}O reaction. The experiment has been performed at the Laboratory for Underground Nuclear Astrophysics (LUNA) 400-kV accelerator placed deep underground inmore » the Gran Sasso facility in Italy. Using a composite germanium detector, summing corrections have been considerably reduced with respect to previous studies. The cross sections for capture to the ground state and to the 5181, 6172, and 6792 keV excited states in {sup 15}O have been determined at 359, 380, and 399 keV beam energy. In addition, the branching ratios for the decay of the 278-keV resonance have been remeasured.« less

Integer ratios of S{sub n}/E{sub n} in {sup 40}Ca+n resonances suggesting two-oscillator excitations in the target nucleus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ohkubo, Makio

2009-08-15

In s-wave neutron resonances of {sup 40}Ca at E{sub n}{<=}2.5 MeV, S{sub n}/E{sub n} for many levels is found to be of the form 17(n/m) where n, m are small integers. Statistical tests show small probabilities for the observed dispositions of many levels at E{sub n}=(j/k)(1/70)G (j, k; small integers). To meet the requirement of time periodicity of the compound nucleus at resonance, a breathing model is developed, where the excitation energies E{sub x} are written as a sum of inverse integers; E{sub x}=S{sub n}+E{sub n}=G{sigma}(1/k) (k: integer). In {sup 40}Ca+n, the separation energy S{sub n}=8362 keV is written asmore » S{sub n}=(17/70)G=(1/7+1/10)G, where G=34.4 MeV. G is almost equal to the Fermi energy of the nucleus. It is suggested that two oscillators of energy (1/7)G and (1/10)G are excited in {sup 40}Ca by neutron incidence, in which the recurrence energy (1/70)G is resonant with neutrons of energies at (j/k)(1/70)G, forming a simple compound nucleus.« less

Joint CPT and N resonance in compact atomic time standards

NASA Astrophysics Data System (ADS)

Crescimanno, Michael; Hohensee, Michael; Xiao, Yanhong; Phillips, David; Walsworth, Ron

2008-05-01

Currently development efforts towards small, low power atomic time standards use current-modulated VCSELs to generate phase-coherent optical sidebands that interrogate the hyperfine structure of alkali atoms such as rubidium. We describe and use a modified four-level quantum optics model to study the optimal operating regime of the joint CPT- and N-resonance clock. Resonant and non-resonant light shifts as well as modulation comb detuning effects play a key role in determining the optimal operating point of such clocks. We further show that our model is in good agreement with experimental tests performed using Rb-87 vapor cells.

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

DOE PAGES

Pignatari, M.; Zinner, E.; Hoppe, P.; ...

2015-07-30

We compared carbon-rich grains with isotopic anomalies 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 (LD) graphites condensed in the ejecta of core-collapse supernovae. Furthermore, 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. All of the explosion energies and Hmore » concentrations are considered. If the supernova 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 puzzle of the Ne-E(L) component in LD graphite grains. This scenario is attractive for the SiC grains of type AB with 14N/ 15N ratios lower than solar, and provides an alternative solution for SiC grains originally classified as nova grains. Finally, this process may contribute to the production of 14N and 15N in the Galaxy, helping to produce the 14N/ 15N ratio in the solar system.« less

Selective excitation for spectral editing and assignment in separated local field experiments of oriented membrane proteins

NASA Astrophysics Data System (ADS)

Koroloff, Sophie N.; Nevzorov, Alexander A.

2017-01-01

Spectroscopic assignment of NMR spectra for oriented uniformly labeled membrane proteins embedded in their native-like bilayer environment is essential for their structure determination. However, sequence-specific assignment in oriented-sample (OS) NMR is often complicated by insufficient resolution and spectral crowding. Therefore, the assignment process is usually done by a laborious and expensive "shotgun" method involving multiple selective labeling of amino acid residues. Presented here is a strategy to overcome poor spectral resolution in crowded regions of 2D spectra by selecting resolved "seed" residues via soft Gaussian pulses inserted into spin-exchange separated local-field experiments. The Gaussian pulse places the selected polarization along the z-axis while dephasing the other signals before the evolution of the 1H-15N dipolar couplings. The transfer of magnetization is accomplished via mismatched Hartmann-Hahn conditions to the nearest-neighbor peaks via the proton bath. By optimizing the length and amplitude of the Gaussian pulse, one can also achieve a phase inversion of the closest peaks, thus providing an additional phase contrast. From the superposition of the selective spin-exchanged SAMPI4 onto the fully excited SAMPI4 spectrum, the 15N sites that are directly adjacent to the selectively excited residues can be easily identified, thereby providing a straightforward method for initiating the assignment process in oriented membrane proteins.

N-15 tracing helps explaining N leaching losses from contrasting forest ecosystems

NASA Astrophysics Data System (ADS)

Staelens, J.; Rütting, T.; Huygens, D.; Müller, C.; Verheyen, K.; Boeckx, P.

2009-04-01

Despite chronically enhanced nitrogen (N) deposition to forest ecosystems in Europe and NE America, considerable N retention by forests has been observed, reducing N leaching losses. Organic and mineral soil layers typically immobilize more N than the aboveground biomass, but it is unclear which factors determine N retention in forest ecoystems. However, this knowledge is crucial to assess the impact of changing anthropogenic N emissions on future N cycling and N loss of forests. For coniferous and deciduous forest stands at comparable sites, it is known that both N deposition onto the forest floor as well as N loss by leaching below the rooting zone are significantly higher in coniferous stands. In addition, the N loss in coniferous stands is often more enhanced than can be explained by the higher N input only. This suggests lower N retention by coniferous stands, and may be related to differences in litter and soil characteristics, microbial activity, and N uptake by plant roots. To test this hypothesis, we studied the effect of forest type on N retention using 15N tracing techniques: a field tracer experiment and a combination of in situ isotope pool dilution and a tracing model. The N dynamics were examined for two adjacent forest stands (pedunculate oak (Quercus robur L.) and Scots pine (Pinus sylvestris L.)) on a well-drained sandy soil and with a similar stand history, located in a region with high N deposition (Belgium). Input-output N budgets were established by quantifying atmospheric deposition and leaching below the rooting zone, and confirmed the above finding of higher N deposition and disproportionately higher N loss for the pine stand compared to the oak stand. First, the fate of inorganic N within the ecosystems was studied by spraying three pulses of dissolved 15N, either as ammonium or as nitrate, onto the forest floor in 12 plots of 25 m2. The organic and mineral soil layers, tree roots, soil water percolate, ferns, and tree foliage were sampled

Soil N and 15N variation with time in a California annual grassland ecosystem

USGS Publications Warehouse

Brenner, D.L.; Amundson, Ronald; Baisden, W. Troy; Kendall, C.; Harden, J.

2001-01-01

The %N and ??15N values of soils and plants were measured along a chronosequence spanning 3 to 3000 Ky in a California annual grassland. Total soil N decreased with increasing soil age (1.1 to 0.4 kg N m-2) while the mean ?? 15N values of the soil N increased by several ??? from the youngest to oldest sites (+3.5 to +6.2 ???). The ?? 15N values of plants varied along the gradient, reflecting changing soil N pools and differences in the form of N uptake. The decline in total N storage with time is hypothesized to be due to a shift from N to P limitation with increasing soil age. The general increase in ?? 15N values with time is interpreted using a N mass balance model, and appears to reflect a shift toward an increasing proportional losses of inorganic mineral forms of N (vs. organic forms) with increasing soil age. We develop a quantitative index of this trend (mineral vs. organic forms of N loss) using mass balance considerations and parameters. The %N and ?? 15N values along the California age gradient were compared to the published data for a comparably aged chronosequence in Hawaii. Most striking in this comparison is the observation that the California soil and plant ?? 15N values are several ??? greater than those on comparably aged Hawaiian sites. Multiple explanations are plausible, but assuming the sites have a similar range in ?? 15N values of atmospheric inputs, the isotopic differences suggest that N may be, at least seasonally, in greater excess in the strongly seasonal, semi-arid, California grassland. Copyright ?? 2001 Elsevier Science Ltd.

Properties of Mg and Zn acceptors in MOVPE GaN as studied by optically detected magnetic resonance

NASA Astrophysics Data System (ADS)

Kunzer, M.; Baur, J.; Kaufmann, U.; Schneider, J.; Amano, H.; Akasaki, I.

1997-02-01

We have studied the photoluminescence (PL) and optically detected magnetic resonance (ODMR) of undoped, n-doped and p-doped thin wurtzite GaN layers grown by metal-organic chemical vapor deposition on sapphire substrates. The ODMR data obtained for undoped. Mg-doped and Zn-doped GaN layers provide an insight into the recombination mechanisms responsible for the broad yellow (2.25 eV), the violet (3.15 eV) and the blue (2.8 eV) PL bands, respectively. The ODMR results for Mg and Zn also show that these acceptors do not behave effective mass like and indicate that the acceptor hole is mainly localized in the nearest neighbor shell surrounding the acceptor core. In addition concentration effects in heavily doped GaN:Mg have been studied.

Sequence-specific sup 1 H NMR resonance assignments of Bacillus subtilis HPr: Use of spectra obtained from mutants to resolve spectral overlap

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wittekind, M.; Klevit, R.E.; Reizer, J.

1990-08-07

On the basis of an analysis of two-dimensional {sup 1}H NMR spectra, the complete sequence-specific {sup 1}H NMR assignments are presented for the phosphocarrier protein HPr from the Gram-positive bacterium Bacillus subtilis. During the assignment procedure, extensive use was made of spectra obtained from point mutants of HPr in order to resolve spectral overlap and to provide verification of assignments. Regions of regular secondary structure were identified by characteristic patterns of sequential backbone proton NOEs and slowly exchanging amide protons. B subtilis HPr contains four {beta}-strands that form a single antiparallel {beta}-sheet and two well-defined {alpha}-helices. There are two stretchesmore » of extended backbone structure, one of which contains the active site His{sub 15}. The overall fold of the protein is very similar to that of Escherichia coli HPr determined by NMR studies.« less

Evidence of N*(1535) resonance contribution in the pn{yields}d{phi} reaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cao Xu; Theoretical Physics Center for Sciences Facilities, Chinese Academy of Sciences, Beijing 100049; Graduate University of Chinese Academy of Sciences, Beijing 100049

2009-08-15

The N*(1535) resonance contributions to the pn{yields}d{phi} reaction are evaluated in an effective Lagrangian model. The {pi}-, {eta}-, and {rho}-meson exchange are considered. It is shown that the contributions from {pi}- and {rho}-meson exchange are dominant, while the contribution from {eta}-meson exchange is negligibly small. Our theoretical results reproduce the experimental data of both total cross section and angular distribution well. This is more evidence that the N*(1535) resonance has a large ss component leading to a large coupling to N{phi}, which may be the real origin of the Okubo-Zweig-Iizuka rule violation in the {pi}N and pN reactions.

Consistent Assignment of the Vibrations of Monohalosubstituted Benzenes

NASA Astrophysics Data System (ADS)

Harris, Joe; Andrejeva, Anna; Tuttle, William Duncan; Pugliesi, Igor; Schriever, Christian; Wright, Tim

2014-06-01

When substituted benzenes become a focus of a spectroscopic study there are various well known vibrational labelling schemes present, however it was shown in recent works the description of monohalobenzene vibrations in terms of benzene modes (ie. Wilson notation) is questionable in some cases. A new scheme is presented which uses the motions of monofluorobenzene vibrations as a basis for labelling vibrational assignments of monosubstituted benzenes.d The scheme has been successfully applied to the ground and excited states of toluene and its deuterated-methyl group isotopologue. Here we present the application of the scheme to fluorobenzene and its fully deuterated analogue. One-colour resonance-enhanced multiphoton ionization (REMPI) spectroscopy was employed in order to characterise the fluorobenzene and fluorobenzene-d5 excited state. E. B. Wilson Jr., Phys. Rev., 45, 706 (1934) G .Varsanyi, Assignments of the Vibrational Spectra of Seven Hundred Benzene Derivatives,Wiley, New York, 1974, Vol. I and II I. Pugliesi, N. C. Tonge and M. C. R. Cockett, J. Chem. Phys., 129, 104303 (2008) A. M. Gardner and T. G. Wright, J. Chem. Phys., 135,114305 (2011) A. M. Gardner, A. M. Green, V. M. Tame-Reyes, V. H. K. Wilton and T. G. Wright, 138, 134303 (2013) A. M. Gardner, A. M. Green, V. M. Tame-Reyes, K. L. Reid, J. A. Davies, V. H. K. Wilton and T. G. Wright, manuscript accepted

Refining cotton-wick method for 15N plant labelling.

NASA Astrophysics Data System (ADS)

Fustec, Joëlle; Mahieu, Stéphanie

2010-05-01

The symbiosis Fabaceae/Rhizobiaceae plays a critical role in the nitrogen cycle. It gives the plant the ability to fix high amounts of atmospheric N. A part of this N can be transferred to the soil via rhizodeposition. The contribution of Fabaceae to the soil N pool is difficult to measure, since it is necessary for assessing N benefits for other crops, for soil biological activity, and for reducing water pollution in sustainable agriculture (Fustec, 2009). The aim of this study was to test and improve the reliability of the 15N cotton-wick method for measuring the soil N derived from plant rhizodeposition (Mahieu et al., 2007). The effects of the concentration of the 15N-urea labelling solution and of the feeding frequency (continuous or pulses) on the assessment of nitrogen rhizodeposition were studied in two greenhouse experiments using the field pea (Pisum sativum L.) and the non-nodulating isoline P2. The plant parts and the soil were prepared for 15N:14N measurements for assessing N rhizodeposition (Mahieu et al., 2009). The fraction of plants' belowground nitrogen allocated to rhizodeposition in both Frisson pea and P2 was 20 to more than 50% higher when plants were labelled continuously than when they were labelled using fortnightly pulses. Our results suggested that when 15N root enrichment was high, nitrogen rhizodeposition was underestimated only for plants that were 15N-fed by fortnightly pulses, and not in plants 15N-fed continuously. This phenomenon was especially observed for plants relying on symbiotic N fixation for N acquisition; it may be linked to the concentration of the labelling solution. In conclusion, N rhizodeposition assessment was strongly influenced by the 15N-feeding frequency and the concentration of the labelling solution. The estimation of N rhizodeposition was more reliable when plants were labelled continuously with a dilute solution of 15N urea. Fustec et al. 2009. Agron. Sustain. Dev., DOI 10.1051/agro/2009003, in press. Mahieu

Effects of Be acceptors on the spin polarization of carriers in p-i-n resonant tunneling diodes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Awan, I. T.; Galvão Gobato, Y.; Galeti, H. V. A.

In this paper, we have investigated the effect of Be acceptors on the electroluminescence and the spin polarization in GaAs/AlAs p-i-n resonant tunneling diodes. The quantum well emission comprise two main lines separated by ∼20 meV attributed to excitonic and Be-related transitions, which intensities show remarkably abrupt variations at critical voltages, particularly at the electron resonant peak where it shows a high-frequency bistability. The circular-polarization degree of the quantum-well electroluminescence also shows strong and abrupt variations at the critical bias voltages and it attains relatively large values (of ∼−75% at 15 T). These effects may be explored to design novel devices formore » spintronic applications such as a high-frequency spin-oscillators.« less

Beam-target helicity asymmetry for γ → n → → π - p in the N * resonance region

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ho, D.; Peng, P.; Bass, C.

In this paper, we report the first beam-target double-polarization asymmetries in themore » $$\\gamma + n(p) \\rightarrow \\pi^- + p(p)$$ reaction spanning the nucleon resonance region from invariant mass $W$= $1500$ to $2300$ MeV. Circularly polarized photons and longitudinally polarized deuterons in $HD$ have been used with the CLAS detector at Jefferson Lab. The exclusive final state has been extracted using three very different analysis techniques that show excellent agreement, and these have been used to deduce the $E$ polarization observable for an effective neutron target. These results have been incorporated into new partial wave analyses, and have led to revised values for several $$\\gamma nN^*$$ resonance photo-couplings.« less

Beam-target helicity asymmetry for γ → n → → π - p in the N * resonance region

DOE PAGES

Ho, D.; Peng, P.; Bass, C.; ...

2017-06-16

In this paper, we report the first beam-target double-polarization asymmetries in themore » $$\\gamma + n(p) \\rightarrow \\pi^- + p(p)$$ reaction spanning the nucleon resonance region from invariant mass $W$= $1500$ to $2300$ MeV. Circularly polarized photons and longitudinally polarized deuterons in $HD$ have been used with the CLAS detector at Jefferson Lab. The exclusive final state has been extracted using three very different analysis techniques that show excellent agreement, and these have been used to deduce the $E$ polarization observable for an effective neutron target. These results have been incorporated into new partial wave analyses, and have led to revised values for several $$\\gamma nN^*$$ resonance photo-couplings.« less

Beam-Target Helicity Asymmetry for γ → n → → π - p in the N * Resonance Region

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ho, D.; Peng, P.; Bass, C.

2017-06-01

We report the first beam-target double-polarization asymmetries in the gamma+n(p)->pi(-)+p(p) reaction spanning the nucleon resonance region from invariant mass W=1500 to 2300 MeV. Circularly polarized photons and longitudinally polarized deuterons in solid hydrogen deuteride (HD) have been used with the CEBAF Large Acceptance Spectrometer (CLAS) at Jefferson Lab. The exclusive final state has been extracted using three very different analyses that show excellent agreement, and these have been used to deduce the E polarization observable for an effective neutron target. These results have been incorporated into new partial wave analyses and have led to significant revisions for several gamma nN*more » resonance photocouplings.« less

Application of C30B15N15 heterofullerene in the isoniazid drug delivery: DFT studies

NASA Astrophysics Data System (ADS)

Hazrati, Mehrnoosh Khodam; Bagheri, Zargham; Bodaghi, Ali

2017-05-01

Using density functional theory, we have investigated the potential application of a C30B15N15 heterofullerene in anti-cancer isoniazid drug delivery. It was found that isoniazid prefers to attach via its -NH2 group to a boron atom of the C30B15N15 with releasing a large energy of about 21.91 kcal/mol. Our partial density of states analysis demonstrates that the boron atoms significantly contribute in generation of virtual orbitals of C30B15N15 fullerene, indicating that these atoms will be suitable for nucleophilic attack rather than carbon atoms. In addition to the large released energy, the electronic properties C30B15N15 are significantly sensitive to the isoniazid attachment which can recognize the drug trajectory by affecting the fluorescence emission properties. Unlike, different nanostructures whose structures need to be manipulated to be suitable for drug delivery, the C30B15N15 fullerene can be used in the pristine form. We proposed a drug release mechanism in cancer tissues, representing that in the low pH of the cancer cells the drug and C30B15N15 fullerene are considerably protonated, thereby separating the drug from the surface of the fullerene. The reaction mechanism of the drug with the fullerene is changed from covalence in natural environment to hydrogen bonding in acidic cancer cells.

Elucidating mineralisation-immobilisation dynamics in a grassland soil using triple 15N labelling in the field combined with a 15N tracing laboratory approach

NASA Astrophysics Data System (ADS)

Kleineidam, Kristina; Müller, Christoph

2017-04-01

Mineralisation is a key N transformation process supplying reactive nitrogen (N) to terrestrial ecosystems. The various soil organic matter fractions contribute to the total mineralisation according to their turnover characteristic. However, the exact mechanism and the gross dynamics of the various processes are not well understood. In this study we investigated the mineralisation-immobilisation dynamics in a grassland soil by a combined field-laboratory study. Eighteen microplots were established at a field site receiving 50 kg N ha-1 as ammonium nitrate. In nine (3 x 3) respective plots the ammonium, or the nitrate, or both moieties were 15N labelled at 60 atom%. Previous studies with this soil showed that rapid turnover occurred and available N would partly be immobilised by the microbial biomass increasing the 15N label of the soil organic nitrogen pool in the field. After one year, soil samples were taken from the 15N treated and the so far non-labelled plots and examined in a laboratory study (for details of the setup see: Müller et al., 2004). While the previously differentially 15N labelled field soils were now supplied with unlabelled ammonium nitrate, the previously unlabelled soils were now treated with either 15N labelled ammonium nitrate similar to the 15N treatments established in the field, resulting in six different 15N treatments in total. The incubation study was carried out over a two week period and data were analysed with the Ntrace model to quantify the simultaneously occurring gross N transformations while optimizing a single parameter set for all six treatments. Thus, the appearance of 15N from the previously labelled soils and the dilution of the 15N in the recently labelled treatments were assumed to be driven by the same processes and activities and were used to constrain the 15N tracing model. This approach allowed us to estimate the individual gross N transformation rates with a much higher accuracy than if only a common triple

Nitrogen and 15N in the Mer Bleue peatland

NASA Astrophysics Data System (ADS)

Moore, Tim

2017-04-01

Although much of our attention in peatlands has focussed on carbon, as CO2, CH4 and DOC processing and fluxes, N plays an important role in the functioning of these ecosystems. Here, I present information on the distribution of N and 15N in plant and peat tissues and relate them to the cycling of N. N concentration in foliar tissues, ranged from 0.67 to 1.3% in evergreen shrubs and trees and mosses with little seasonal variation, and with a strong seasonal variation from 0.5 to 3.5% in the deciduous forbs, shrubs and trees, with a strong overall relationship to [chlorophyll]. Although the proportion of shrubs and mosses varied with microtopography the spatial foliar mass of N varied little with water table position, resulting in minor spatial variations in photosynthetic potential. Decomposition of plant tissues through litter to peat resulted in a decrease in the C:N ratio from about 50:1 to about 30:1 at the base of the profile, representing peat about 8000 yr old. This marginally larger loss of N through decomposition (mainly as TDN, 0.4 g N m-2 yr-1) compared to C produced a long-term N accumulation rate of 0.9 g N m-2 yr-1, being smaller in the bog phase, 0.6 N m-2 yr-1, and over past 150 yr, 0.8 g N m-2 yr-1. Although N is 'hard won' through N2 fixation, northern peatlands are significant global sinks of N and have limited N availability. del15N in foliar tissues ranged from -4 to -9 ‰ in evergreen and deciduous shrubs and trees, from -4 to -5 ‰ in mosses and from -1 to +1 ‰ in sedges and forbs. This appears to be a function of the mycorhizzal infection of the shrubs and trees, compared to sedges and forbs and the values for mosses may partially reflect the signature of atmospheric N deposition. There was no strong correlation between foliar [N] and del15N. In peat profiles from bog and fen sections of Mer Bleue, del15N values in peat fell from -5 to -2 ‰ in the top 10 cm to values of -1 to +1 ‰ at a depth of 40 cm and remained close to 0 ‰ below

Formularity: Software for Automated Formula Assignment of Natural and Other Organic Matter from Ultrahigh-Resolution Mass Spectra

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tolić, Nikola; Liu, Yina; Liyu, Andrey

Ultrahigh-resolution mass spectrometry, such as Fourier transform ion-cyclotron resonance mass spectrometry (FT-ICR MS), can resolve thousands of molecular ions in complex organic matrices. A Compound Identification Algorithm (CIA) was previously developed for automated elemental formula assignment for natural organic matter (NOM). In this work we describe a user friendly interface for CIA, titled Formularity, which includes an additional functionality to perform search of formulas based on an Isotopic Pattern Algorithm (IPA). While CIA assigns elemental formulas for compounds containing C, H, O, N, S, and P, IPA is capable of assigning formulas for compounds containing other elements. We used halogenatedmore » organic compounds (HOC), a chemical class that is ubiquitous in nature as well as anthropogenic systems, as an example to demonstrate the capability of Formularity with IPA. A HOC standard mix was used to evaluate the identification confidence of IPA. The HOC spike in NOM and tap water were used to assess HOC identification in natural and anthropogenic matrices. Strategies for reconciliation of CIA and IPA assignments are discussed. Software and sample databases with documentation are freely available from the PNNL OMICS software repository https://omics.pnl.gov/software/formularity.« less

Acoustic resonator with Al electrodes on an AlN layer and using a GaAs substrate

DOEpatents

Kline, Gerald R.; Lakin, Kenneth M.

1985-12-03

A method of fabricating an acoustic wave resonator wherein all processing steps are accomplished from a single side of said substrate. The method involves deposition of a multi-layered Al/AlN structure on a GaAs substrate followed by a series of fabrication steps to define a resonator from said composite. The resulting resonator comprises an AlN layer between two Al layers and another layer of AlN on an exterior of one of said Al layers.

Simple approach for the preparation of (15-15)N2-enriched water for nitrogen fixation assessments: evaluation, application and recommendations.

PubMed

Klawonn, Isabell; Lavik, Gaute; Böning, Philipp; Marchant, Hannah K; Dekaezemacker, Julien; Mohr, Wiebke; Ploug, Helle

2015-01-01

Recent findings revealed that the commonly used (15)N2 tracer assay for the determination of dinitrogen (N2) fixation can underestimate the activity of aquatic N2-fixing organisms. Therefore, a modification to the method using pre-prepared (15-15)N2-enriched water was proposed. Here, we present a rigorous assessment and outline a simple procedure for the preparation of (15-15)N2-enriched water. We recommend to fill sterile-filtered water into serum bottles and to add (15-15)N2 gas to the water in amounts exceeding the standard N2 solubility, followed by vigorous agitation (vortex mixing ≥ 5 min). Optionally, water can be degassed at low-pressure (≥950 mbar) for 10 min prior to the (15-15)N2 gas addition to indirectly enhance the (15-15)N2 concentration. This preparation of (15-15)N2-enriched water can be done within 1 h using standard laboratory equipment. The final (15)N-atom% excess was 5% after replacing 2-5% of the incubation volume with (15-15)N2-enriched water. Notably, the addition of (15-15)N2-enriched water can alter levels of trace elements in the incubation water due to the contact of (15-15)N2-enriched water with glass, plastic and rubber ware. In our tests, levels of trace elements (Fe, P, Mn, Mo, Cu, Zn) increased by up to 0.1 nmol L(-1) in the final incubation volume, which may bias rate measurements in regions where N2 fixation is limited by trace elements. For these regions, we tested an alternative way to enrich water with (15-15)N2. The (15-15)N2 was injected as a bubble directly to the incubation water, followed by gentle shaking. Immediately thereafter, the bubble was replaced with water to stop the (15-15)N2 equilibration. This approach achieved a (15)N-atom% excess of 6.6 ± 1.7% when adding 2 mL (15-15)N2 per liter of incubation water. The herein presented methodological tests offer guidelines for the (15)N2 tracer assay and thus, are crucial to circumvent methodological draw-backs for future N2 fixation assessments.

The AGB star nucleosynthesis in the light of the recent {sup 17}O(p,α){sup 14}N and {sup 18}O(p,α){sup 15}N reaction rate determinations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Palmerini, S.; Sergi, M. L.; La Cognata, M.

2015-02-24

Presolar grains form in the cold and dusty envelopes of Asymptotic Giant Branch (AGB) stars. These solides, once that have been ejected by stellar winds, come to us as inclusions in meteorites providing invaluable benchmarks and constraints for our knowledge of low temeperature H-burning in stars. The Trojan Horse Method (THM) has been used to investigate the low-energy cross sections of the {sup 17}O(p,α){sup 14}N and {sup 18}O(p,α){sup 15}N reactions. Moreover, the strength of the 65 keV resonance in the {sup 17}O(p,α){sup 14}N reaction, measured by means of the THM, has been used to renormalize the corresponding resonance strength inmore » the {sup 17}O+p radiative capture channel. The new estimates of the reaction rates have been introduced into calculations of AGB star nucleosynthesis and the results have been compared with geochemical analysis of 'presolar' grains to determine their impact on astrophysical environments.« less

Novel DNA packaging recognition in the unusual bacteriophage N15

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feiss, Michael; Geyer, Henriette, E-mail: henriettegeyer@gmail.com; Division of Viral Infections, Robert Koch Institute, Berlin

Phage lambda's cosB packaging recognition site is tripartite, consisting of 3 TerS binding sites, called R sequences. TerS binding to the critical R3 site positions the TerL endonuclease for nicking cosN to generate cohesive ends. The N15 cos (cos{sup N15}) is closely related to cos{sup λ}, but whereas the cosB{sup N15} subsite has R3, it lacks the R2 and R1 sites and the IHF binding site of cosB{sup λ}. A bioinformatic study of N15-like phages indicates that cosB{sup N15} also has an accessory, remote rR2 site, which is proposed to increase packaging efficiency, like R2 and R1 of lambda. N15more » plus five prophages all have the rR2 sequence, which is located in the TerS-encoding 1 gene, approximately 200 bp distal to R3. An additional set of four highly related prophages, exemplified by Monarch, has R3 sequence, but also has R2 and R1 sequences characteristic of cosB–λ. The DNA binding domain of TerS-N15 is a dimer. - Highlights: • There are two classes of DNA packaging signals in N15-related phages. • Phage N15's TerS binding site: a critical site and a possible remote accessory site. • Viral DNA recognition signals by the λ-like bacteriophages: the odd case of N15.« less

Nature of isomerism of solid isothiourea salts, inhibitors of nitric oxide synthases, as studied by 1H-14N nuclear quadrupole double resonance, X-ray, and density functional theory/quantum theory of atoms in molecules.

PubMed

Latosińska, J N; Latosińska, M; Seliger, J; Žagar, V; Maurin, J K; Kazimierczuk, Z

2012-02-09

Isothioureas, inhibitors of nitric oxide synthases, have been studied experimentally in solid state by nuclear quadrupole double resonance (NQDR) and X-ray methods and theoretically by the quantum theory of atoms in molecules/density functional theory. Resonance frequencies on (14)N have been detected and assigned to particular nitrogen sites in each molecule. The crystal packings of (S)-3,4-dichlorobenzyl-N-methylisothiouronium chloride with the disordered chlorine positions in benzene ring and (S)-butyloisothiouronium bromide have been resolved in X-ray diffraction studies. (14)N NQDR spectra have been found good indicators of isomer type and strength of intra- or intermolecular N-H···X (X = Cl, Br) interactions. From among all salts studied, only for (S)-2,3,4,5,6-pentabromobenzylisothiouronium chloride are both nitrogen sites equivalent, which has been explained by the slow exchange. This unique structural feature can be a key factor in the high biological activity of (S)-2,3,4,5,6-pentabromobenzylisothiouronium salts.

Neutron Resonance Spin Determination Using Multi-Segmented Detector DANCE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baramsai, B.; Mitchell, G. E.; Chyzh, A.

2011-06-01

A sensitive method to determine the spin of neutron resonances is introduced based on the statistical pattern recognition technique. The new method was used to assign the spins of s-wave resonances in {sup 155}Gd. The experimental neutron capture data for these nuclei were measured with the DANCE (Detector for Advanced Neutron Capture Experiment) calorimeter at the Los Alamos Neutron Science Center. The highly segmented calorimeter provided detailed multiplicity distributions of the capture {gamma}-rays. Using this information, the spins of the neutron capture resonances were determined. With these new spin assignments, level spacings are determined separately for s-wave resonances with J{supmore » {pi}} = 1{sup -} and 2{sup -}.« less

"Ask Ernö": a self-learning tool for assignment and prediction of nuclear magnetic resonance spectra.

PubMed

Castillo, Andrés M; Bernal, Andrés; Dieden, Reiner; Patiny, Luc; Wist, Julien

2016-01-01

We present "Ask Ernö", a self-learning system for the automatic analysis of NMR spectra, consisting of integrated chemical shift assignment and prediction tools. The output of the automatic assignment component initializes and improves a database of assigned protons that is used by the chemical shift predictor. In turn, the predictions provided by the latter facilitate improvement of the assignment process. Iteration on these steps allows Ask Ernö to improve its ability to assign and predict spectra without any prior knowledge or assistance from human experts. This concept was tested by training such a system with a dataset of 2341 molecules and their (1)H-NMR spectra, and evaluating the accuracy of chemical shift predictions on a test set of 298 partially assigned molecules (2007 assigned protons). After 10 iterations, Ask Ernö was able to decrease its prediction error by 17 %, reaching an average error of 0.265 ppm. Over 60 % of the test chemical shifts were predicted within 0.2 ppm, while only 5 % still presented a prediction error of more than 1 ppm. Ask Ernö introduces an innovative approach to automatic NMR analysis that constantly learns and improves when provided with new data. Furthermore, it completely avoids the need for manually assigned spectra. This system has the potential to be turned into a fully autonomous tool able to compete with the best alternatives currently available.Graphical abstractSelf-learning loop. Any progress in the prediction (forward problem) will improve the assignment ability (reverse problem) and vice versa.

Optimal processor assignment for pipeline computations

NASA Technical Reports Server (NTRS)

Nicol, David M.; Simha, Rahul; Choudhury, Alok N.; Narahari, Bhagirath

1991-01-01

The availability of large scale multitasked parallel architectures introduces the following processor assignment problem for pipelined computations. Given a set of tasks and their precedence constraints, along with their experimentally determined individual responses times for different processor sizes, find an assignment of processor to tasks. Two objectives are of interest: minimal response given a throughput requirement, and maximal throughput given a response time requirement. These assignment problems differ considerably from the classical mapping problem in which several tasks share a processor; instead, it is assumed that a large number of processors are to be assigned to a relatively small number of tasks. Efficient assignment algorithms were developed for different classes of task structures. For a p processor system and a series parallel precedence graph with n constituent tasks, an O(np2) algorithm is provided that finds the optimal assignment for the response time optimization problem; it was found that the assignment optimizing the constrained throughput in O(np2log p) time. Special cases of linear, independent, and tree graphs are also considered.

3μm - 1.6μm Double Resonance Spectroscopy of CH_4

NASA Astrophysics Data System (ADS)

Schwartz, George; Belaas, Erik; Yang, Shaoyue; Lehmann, Kevin

2016-06-01

The Near-IR Spectrum of CH_4 is dense with many overlapping bands that perturb each other by vibrational and ro-vibrational interactions. Assignments of the individual lines are needed in order to simulate the spectrum as a function of pressure and temperature, as needed in the search for CH_4 in extrasolar planets. Both the group at the University College, London^1 and that at the University of Reins^2 have produced theoretical spectra that allows simulation up to the high temperatures expected on ``Hot Jupiters''. The accuracy of these theoretical spectra need to be further tested. Because CH_4 is a light spherical top, assignment of its perturbed spectra is a formable challenge as none of the lines allowed in the rigid rotor approximation have ground vibrational state combination differences. We are using IR-IR double resonance to observe modulation in the strength of near-IR absorption caused by a modulation of a 3 μm OPO beam that is tuned to a particular transition in the C-H stretching fundamental of CH_4. This produces V-type double resonance transitions (which share the lower state with the pump transition), which provides firm assignments for lines normally observed in absorption in the near-IR. We also observe sequential double resonance which reveals transitions that have a known rotational level of the ν_3 fundamental as the lower state and reaches final states in the 9000 cm-1 spectral region. These are states of A, E, F_1 vibrational symmetries which are forbidden in transitions from the ground vibrational state. These 3 level double resonance transitions are Doppler Free and have a linewidth of ˜10 MHz due to a combination of near-IR laser jitter and power broadening of the mid-IR transition. We also observed many 4-level double resonance transitions that we have tentatively assigned as arising from the ν_4 fundamental level. These are distinguished from the 3-level double resonance transitions by they being Doppler broadened and having a large

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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, themore » 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.« less

Identifying N fertilizer regime and vegetable production system in tropical Brazil using (15) N natural abundance.

PubMed

Inácio, Caio T; Urquiaga, Segundo; Chalk, Phillip M; Mata, Maria Gabriela F; Souza, Paulo O

2015-12-01

This study was conducted in areas of vegetable production in tropical Brazil, with the objectives of (i) measuring the variation in δ(15)  N in soils, organic N fertilizer sources and lettuce (Lactuca sativa L.) from different farming systems, (ii) measuring whether plant δ(15)  N can differentiate organic versus conventional lettuce and (iii) identifying the factors affecting lettuce δ(15)  N. Samples of soil, lettuce and organic inputs were taken from two organic, one conventional and one hydroponic farm. The two organic farms had different N-sources with δ(15)  N values ranging from 0.0 to +14.9‰ (e.g. leguminous green manure and animal manure compost, respectively), and differed significantly (P < 0.05) in lettuce δ(15)  N (+9.2 ± 1.1‰ and +14.3 ± 1.0‰). Conventional lettuce δ(15)  N (+8.5 ± 2.7‰) differed from hydroponic lettuce δ(15)  N (+4.5 ± 0.2‰) due to manure inputs. The N from leguminous green manure made a small contribution to the N nutrition of lettuce in the multi-N-source organic farm. To differentiate organic versus conventional farms using δ(15)  N the several subsets of mode of fertilization should be considered. Comparisons of δ(15)  N of soil, organic inputs and lettuce allowed a qualitative analysis of the relative importance of different N inputs. © 2015 Society of Chemical Industry.

Resonant Coherent Excitation of Hydrogen-Like Ar Ions to the n =: 3 States

NASA Astrophysics Data System (ADS)

Azuma, T.; Ito, T.; Takabayashi, Y.; Komaki, K.; Yamazaki, Y.; Yamazaki, Y.; Takada, E.; Murakami, T.

We have succeeded in observing resonant coherent excitaion (RCE) of 1s electrons to the n = 3 states in 390 MeV/u hydrogen-like Ar17+ ions planar channeled in a silicon crystal through measurements of the charge-state distribution of ions transmitting the crystal. Furthermore, we directly confirmed RCE to the n = 3 states by observing the enhancement of the de-excitation X-rays, i.e., Kβ X-rays under the resonance condition. The resonance profiles of the charge-state distribution as functions of the incident angle to the crystal, which uniquely relates with the transition energy, have a characteristic structure consisting of several peaks. Compared with the profile of RCE to the n = 2 states, the present profiles show a large peak shift from the j = 1/2 and 3/2 levels in vacuum, and the profiles are much wider than those expected from the Stark-split level structure of the n = 3 manifolds due to the position- (distance from the channel center in the planar channel) dependent strong static field in the crystal.

Ecosystem N distribution and δ15N during a century of forest regrowth after agricultural abandonment

USGS Publications Warehouse

Compton, J.E.; Hooker, T.D.; Perakis, S.S.

2007-01-01

Stable isotope ratios of terrestrial ecosystem nitrogen (N) pools reflect internal processes and input–output balances. Disturbance generally increases N cycling and loss, yet few studies have examined ecosystem δ15N over a disturbance-recovery sequence. We used a chronosequence approach to examine N distribution and δ15N during forest regrowth after agricultural abandonment. Site ages ranged from 10 to 115 years, with similar soils, climate, land-use history, and overstory vegetation (white pine Pinus strobus). Foliar N and δ15N decreased as stands aged, consistent with a progressive tightening of the N cycle during forest regrowth on agricultural lands. Over time, foliar δ15N became more negative, indicating increased fractionation along the mineralization–mycorrhizal–plant uptake pathway. Total ecosystem N was constant across the chronosequence, but substantial internal N redistribution occurred from the mineral soil to plants and litter over 115 years (>25% of ecosystem N or 1,610 kg ha−1). Temporal trends in soil δ15N generally reflected a redistribution of depleted N from the mineral soil to the developing O horizon. Although plants and soil δ15N are coupled over millennial time scales of ecosystem development, our observed divergence between plants and soil suggests that they can be uncoupled during the disturbance-regrowth sequence. The approximate 2‰ decrease in ecosystem δ15N over the century scale suggests significant incorporation of atmospheric N, which was not detected by traditional ecosystem N accounting. Consideration of temporal trends and disturbance legacies can improve our understanding of the influence of broader factors such as climate or N deposition on ecosystem N balances and δ15N.

Assessment of Prospectively Assigned Likert Scores for Targeted Magnetic Resonance Imaging-Transrectal Ultrasound Fusion Biopsies in Patients with Suspected Prostate Cancer.

PubMed

Costa, Daniel N; Lotan, Yair; Rofsky, Neil M; Roehrborn, Claus; Liu, Alexander; Hornberger, Brad; Xi, Yin; Francis, Franto; Pedrosa, Ivan

2016-01-01

We assess the performance of prospectively assigned magnetic resonance imaging based Likert scale scores for the detection of clinically significant prostate cancer, and analyze the pre-biopsy imaging variables associated with increased cancer detection using targeted magnetic resonance imaging-transrectal ultrasound fusion biopsy. In this retrospective review of prospectively generated data including men with abnormal multiparametric prostate magnetic resonance imaging (at least 1 Likert score 3 or greater lesion) who underwent subsequent targeted magnetic resonance imaging-transrectal ultrasound fusion biopsy, we determined the association between different imaging variables (Likert score, lesion size, lesion location, prostate volume, radiologist experience) and targeted biopsy positivity rate. We also compared the detection of clinically significant cancer according to Likert scale scores. Tumors with high volume (50% or more of any core) Gleason score 3+4 or any tumor with greater Gleason score were considered clinically significant. Each lesion served as the elementary unit for analysis. We used logistic regression for univariate and multivariate (stepwise selection) analysis to assess for an association between targeted biopsy positivity rate and each tested variable. The relationship between Likert scale and Gleason score was evaluated using the Spearman correlation coefficient. A total of 161 men with 244 lesions met the study eligibility criteria. Targeted biopsies diagnosed cancer in 41% (66 of 161) of the men and 41% (99 of 244) of the lesions. The Likert score was the strongest predictor of targeted biopsy positivity (OR 3.7, p <0.0001). Other imaging findings associated with a higher targeted biopsy positivity rate included smaller prostate volume (OR 0.7, p <0.01), larger lesion size (OR 2.2, p <0.001) and anterior location (OR 2.0, p=0.01). On multiple logistic regression analysis Likert score, lesion size and prostate volume were significant

Structure assignment, electronic properties, and magnetism quenching of endohedrally doped neutral silicon clusters, Si(n)Co (n = 10-12).

PubMed

Li, Yejun; Tam, Nguyen Minh; Claes, Pieterjan; Woodham, Alex P; Lyon, Jonathan T; Ngan, Vu Thi; Nguyen, Minh Tho; Lievens, Peter; Fielicke, André; Janssens, Ewald

2014-09-18

The structures of neutral cobalt-doped silicon clusters have been assigned by a combined experimental and theoretical study. Size-selective infrared spectra of neutral Si(n)Co (n = 10-12) clusters are measured using a tunable IR-UV two-color ionization scheme. The experimental infrared spectra are compared with calculated spectra of low-energy structures predicted at the B3P86 level of theory. It is shown that the Si(n)Co (n = 10-12) clusters have endohedral caged structures, where the silicon frameworks prefer double-layered structures encapsulating the Co atom. Electronic structure analysis indicates that the clusters are stabilized by an ionic interaction between the Co dopant atom and the silicon cage due to the charge transfer from the silicon valence sp orbitals to the cobalt 3d orbitals. Strong hybridization between the Co dopant atom and the silicon host quenches the local magnetic moment on the encapsulated Co atom.

42 CFR 433.146 - Rights assigned; assignment method.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 42 Public Health 4 2013-10-01 2013-10-01 false Rights assigned; assignment method. 433.146 Section 433.146 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN... Assignment of Rights to Benefits § 433.146 Rights assigned; assignment method. (a) Except as specified in...

42 CFR 433.146 - Rights assigned; assignment method.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 42 Public Health 4 2011-10-01 2011-10-01 false Rights assigned; assignment method. 433.146 Section 433.146 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN... Assignment of Rights to Benefits § 433.146 Rights assigned; assignment method. (a) Except as specified in...

42 CFR 433.146 - Rights assigned; assignment method.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 42 Public Health 4 2010-10-01 2010-10-01 false Rights assigned; assignment method. 433.146 Section 433.146 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN... Assignment of Rights to Benefits § 433.146 Rights assigned; assignment method. (a) Except as specified in...

Magnetic resonance angiography in infrapopliteal arterial disease: prospective comparison of 1.5 and 3 Tesla magnetic resonance imaging.

PubMed

Diehm, Nicolas; Kickuth, Ralph; Baumgartner, Iris; Srivastav, Sudesh K; Gretener, Silvia; Husmann, Marc J; Jaccard, Yves; Do, Do Dai; Triller, Juergen; Bonel, Harald M

2007-06-01

To prospectively determine the accuracy of 1.5 Tesla (T) and 3 T magnetic resonance angiography (MRA) versus digital subtraction angiography (DSA) in the depiction of infrageniculate arteries in patients with symptomatic peripheral arterial disease. A prospective 1.5 T, 3 T MRA, and DSA comparison was used to evaluate 360 vessel segments in 10 patients (15 limbs) with chronic symptomatic peripheral arterial disease. Selective DSA was performed within 30 days before both MRAs. The accuracy of 1.5 T and 3 T MRA was compared with DSA as the standard of reference by consensus agreement of 2 experienced readers. Signal-to-noise ratios (SNR) and signal-difference-to-noise ratios (SDNRs) were quantified. No significant difference in overall image quality, sufficiency for diagnosis, depiction of arterial anatomy, motion artifacts, and venous overlap was found comparing 1.5 T with 3 T MRA (P > 0.05 by Wilcoxon signed rank and as by Cohen k test). Overall sensitivity of 1.5 and 3 T MRA for detection of significant arterial stenosis was 79% and 82%, and specificity was 87% and 87% for both modalities, respectively. Interobserver agreement was excellent k > 0.8, P < 0.05) for 1.5 T as well as for 3 T MRA. SNR and SDNR were significantly increased using the 3 T system (average increase: 36.5%, P < 0.032 by t test, and 38.5%, P < 0.037 respectively). Despite marked improvement of SDNR, 3 T MRA does not yet provide a significantly higher accuracy in diagnostic imaging of atherosclerotic lesions below the knee joint as compared with 1.5 T MRA.

Expansion of antimonato polyoxovanadates with transition metal complexes: (Co(N3C5H15)2)2[{Co(N3C5H15)2}V15Sb6O42(H2O)]·5H2O and (Ni(N3C5H15)2)2[{Ni(N3C5H15)2}V15Sb6O42(H2O)]·8H2O.

PubMed

Antonova, Elena; Näther, Christian; Kögerler, Paul; Bensch, Wolfgang

2012-02-20

Two new polyoxovanadates (Co(N(3)C(5)H(15))(2))(2)[{Co(N(3)C(5)H(15))(2)}V(15)Sb(6)O(42)(H(2)O)]·5H(2)O (1) and (Ni(N(3)C(5)H(15))(2))(2)[{Ni(N(3)C(5)H(15))(2)}V(15)Sb(6)O(42)(H(2)O)]·8H(2)O (2) (N(3)C(5)H(15) = N-(2-aminoethyl)-1,3-propanediamine) were synthesized under solvothermal conditions and structurally characterized. In both structures the [V(15)Sb(6)O(42)(H(2)O)](6-) shell displays the main structural motif, which is strongly related to the {V(18)O(42)} archetype cluster. Both compounds crystallize in the triclinic space group P1 with a = 14.3438(4), b = 16.6471(6), c = 18.9186(6) Å, α = 87.291(3)°, β = 83.340(3)°, γ = 78.890(3)°, and V = 4401.4(2) Å(3) (1) and a = 14.5697(13), b = 15.8523(16), c = 20.2411(18) Å, α = 86.702(11)°, β = 84.957(11)°, γ = 76.941(11)°, and V = 4533.0(7) Å(3) (2). In the structure of 1 the [V(15)Sb(6)O(42)(H(2)O)](6-) cluster anion is bound to a [Co(N(3)C(5)H(15))(2)](2+) complex via a terminal oxygen atom. In the Co(2+)-centered complex, one of the amine ligands coordinates in tridentate mode and the second one in bidentate mode to form a strongly distorted CoN(5)O octahedron. Similarly, in compound 2 an analogous NiN(5)O complex is joined to the [V(15)Sb(6)O(42)(H(2)O)](6-) anion via the same attachment mode. A remarkable difference between the two compounds is the orientation of the noncoordinated propylamine group leading to intermolecular Sb···O contacts in 1 and to Sb···N interactions in 2. In the solid-state lattices of 1 and 2, two additional [M(N(3)C(5)H(15))(2)](2+) complexes act as countercations and are located between the [{M(N(3)C(5)H(15))(2)}V(15)Sb(6)O(42)(H(2)O)](4-) anions. Between the anions and cations strong N-H···O hydrogen bonds are observed. In both compounds the clusters are stacked along the b axis in an ABAB fashion with cations and water molecules occupying the space between the clusters. Magnetic characterization demonstrates that the Ni(2+) and Co(2+) cations do not

Electron spin resonance and proton matrix electron nuclear double resonance studies of N,N,N[prime],N[prime]-tetramethylbenzidine photoionization in sodium and lithium dodecyl sulfate micelles: Structural effects of crown ethers

DOE Office of Scientific and Technical Information (OSTI.GOV)

McManus, H.J.D.; Young Soo Kang; Kevan, L.

1993-01-07

The study of model membrane systems enjoys increasing attention within the area of solar energy research. An electron nuclear double resonance and electron spin resonance study of photogenerated N,N,N[prime],N[prime]-tetramethylbenzidine (TMB) cation in frozen suspensions of lithium (LDS) and sodium (SDS) dodecyl sulfate micelles containing various concentrations of cyclic polyethers was undertaken. The relative location of the TMB cation within the organic aggregate was determined from the proton matrix ENDOR line width at 142 K. A broader line width was observed in LDS compared to SDS micelles, which is due to the fact that the larger lithium cation opens the micellarmore » interface resulting in increased hydration and deeper solubilization of TMB. The proton matrix ENDOR line width decreased upon addition of crown ethers. This decrease may be explained by displacement of the TMB toward the interface as a result of the decrease in ionic strength caused by the complexation of the countercations. The photoyield shows a slight increase with addition of crown ethers. This increase is most likely caused by the increase in the effective anionic charge of the micelle effected by the complexation of the sodium or lithium ions by the crown ethers. This increase in the anionic charge mitigates the rate of thermal back electron transfer resulting in an increased photoyield. 54 refs., 6 figs., 2 tabs.« less

Simple approach for the preparation of 15−15N2-enriched water for nitrogen fixation assessments: evaluation, application and recommendations

PubMed Central

Klawonn, Isabell; Lavik, Gaute; Böning, Philipp; Marchant, Hannah K.; Dekaezemacker, Julien; Mohr, Wiebke; Ploug, Helle

2015-01-01

Recent findings revealed that the commonly used 15N2 tracer assay for the determination of dinitrogen (N2) fixation can underestimate the activity of aquatic N2-fixing organisms. Therefore, a modification to the method using pre-prepared 15−15N2-enriched water was proposed. Here, we present a rigorous assessment and outline a simple procedure for the preparation of 15−15N2-enriched water. We recommend to fill sterile-filtered water into serum bottles and to add 15−15N2 gas to the water in amounts exceeding the standard N2 solubility, followed by vigorous agitation (vortex mixing ≥ 5 min). Optionally, water can be degassed at low-pressure (≥950 mbar) for 10 min prior to the 15−15N2 gas addition to indirectly enhance the 15−15N2 concentration. This preparation of 15−15N2-enriched water can be done within 1 h using standard laboratory equipment. The final 15N-atom% excess was 5% after replacing 2–5% of the incubation volume with 15−15N2-enriched water. Notably, the addition of 15−15N2-enriched water can alter levels of trace elements in the incubation water due to the contact of 15−15N2-enriched water with glass, plastic and rubber ware. In our tests, levels of trace elements (Fe, P, Mn, Mo, Cu, Zn) increased by up to 0.1 nmol L−1 in the final incubation volume, which may bias rate measurements in regions where N2 fixation is limited by trace elements. For these regions, we tested an alternative way to enrich water with 15−15N2. The 15−15N2 was injected as a bubble directly to the incubation water, followed by gentle shaking. Immediately thereafter, the bubble was replaced with water to stop the 15−15N2 equilibration. This approach achieved a 15N-atom% excess of 6.6 ± 1.7% when adding 2 mL 15−15N2 per liter of incubation water. The herein presented methodological tests offer guidelines for the 15N2 tracer assay and thus, are crucial to circumvent methodological draw-backs for future N2 fixation assessments. PMID:26300853

15N CSA tensors and 15N-1H dipolar couplings of protein hydrophobic core residues investigated by static solid-state NMR

NASA Astrophysics Data System (ADS)

Vugmeyster, Liliya; Ostrovsky, Dmitry; Fu, Riqiang

2015-10-01

In this work, we assess the usefulness of static 15N NMR techniques for the determination of the 15N chemical shift anisotropy (CSA) tensor parameters and 15N-1H dipolar splittings in powder protein samples. By using five single labeled samples of the villin headpiece subdomain protein in a hydrated lyophilized powder state, we determine the backbone 15N CSA tensors at two temperatures, 22 and -35 °C, in order to get a snapshot of the variability across the residues and as a function of temperature. All sites probed belonged to the hydrophobic core and most of them were part of α-helical regions. The values of the anisotropy (which include the effect of the dynamics) varied between 130 and 156 ppm at 22 °C, while the values of the asymmetry were in the 0.32-0.082 range. The Leu-75 and Leu-61 backbone sites exhibited high mobility based on the values of their temperature-dependent anisotropy parameters. Under the assumption that most differences stem from dynamics, we obtained the values of the motional order parameters for the 15N backbone sites. While a simple one-dimensional line shape experiment was used for the determination of the 15N CSA parameters, a more advanced approach based on the ;magic sandwich; SAMMY pulse sequence (Nevzorov and Opella, 2003) was employed for the determination of the 15N-1H dipolar patterns, which yielded estimates of the dipolar couplings. Accordingly, the motional order parameters for the dipolar interaction were obtained. It was found that the order parameters from the CSA and dipolar measurements are highly correlated, validating that the variability between the residues is governed by the differences in dynamics. The values of the parameters obtained in this work can serve as reference values for developing more advanced magic-angle spinning recoupling techniques for multiple labeled samples.

The Contamination of Commercial 15N2 Gas Stocks with 15N–Labeled Nitrate and Ammonium and Consequences for Nitrogen Fixation Measurements

PubMed Central

Dabundo, Richard; Lehmann, Moritz F.; Treibergs, Lija; Tobias, Craig R.; Altabet, Mark A.; Moisander, Pia H.; Granger, Julie

2014-01-01

We report on the contamination of commercial 15-nitrogen (15N) N2 gas stocks with 15N-enriched ammonium, nitrate and/or nitrite, and nitrous oxide. 15N2 gas is used to estimate N2 fixation rates from incubations of environmental samples by monitoring the incorporation of isotopically labeled 15N2 into organic matter. However, the microbial assimilation of bioavailable 15N-labeled N2 gas contaminants, nitrate, nitrite, and ammonium, is liable to lead to the inflation or false detection of N2 fixation rates. 15N2 gas procured from three major suppliers was analyzed for the presence of these 15N-contaminants. Substantial concentrations of 15N-contaminants were detected in four Sigma-Aldrich 15N2 lecture bottles from two discrete batch syntheses. Per mole of 15N2 gas, 34 to 1900 µmoles of 15N-ammonium, 1.8 to 420 µmoles of 15N-nitrate/nitrite, and ≥21 µmoles of 15N-nitrous oxide were detected. One 15N2 lecture bottle from Campro Scientific contained ≥11 µmoles of 15N-nitrous oxide per mole of 15N2 gas, and no detected 15N-nitrate/nitrite at the given experimental 15N2 tracer dilutions. Two Cambridge Isotopes lecture bottles from discrete batch syntheses contained ≥0.81 µmoles 15N-nitrous oxide per mole 15N2, and trace concentrations of 15N-ammonium and 15N-nitrate/nitrite. 15N2 gas equilibrated cultures of the green algae Dunaliella tertiolecta confirmed that the 15N-contaminants are assimilable. A finite-differencing model parameterized using oceanic field conditions typical of N2 fixation assays suggests that the degree of detected 15N-ammonium contamination could yield inferred N2 fixation rates ranging from undetectable, <0.01 nmoles N L−1 d−1, to 530 nmoles N L−1 d−1, contingent on experimental conditions. These rates are comparable to, or greater than, N2 fixation rates commonly detected in field assays. These results indicate that past reports of N2 fixation should be interpreted with caution, and demonstrate that the purity of commercial 15N2

Doubly 15N-substituted diazenylium: THz laboratory spectra and fractionation models

NASA Astrophysics Data System (ADS)

Dore, L.; Bizzocchi, L.; Wirström, E. S.; Degli Esposti, C.; Tamassia, F.; Charnley, S. B.

2017-07-01

Context. Isotopic fractionation in dense molecular cores has been suggested as a possible origin of large 14N/15N ratio variations in solar system materials. While chemical models can explain some observed variations with different fractionation patterns for molecules with -NH or -CN functional groups, they fail to reproduce the observed ratios in diazenylium (N2H+). Aims: Observations of doubly 15N-substituted species could provide important constraints and insights for theoretical chemical models of isotopic fractionation. However, spectroscopic data are very scarce. Methods: The rotational spectra of the fully 15N-substituted isopologues of the diazenylium ion, 15N2H+ and 15N2D+, have been investigated in the laboratory well into the THz region by using a source-modulation microwave spectrometer equipped with a negative glow discharge cell. An extended chemical reaction network has been used to estimate what ranges of 15N fractionation in doubly 15N-substituted species could be expected in the interstellar medium (ISM). Results: For each isotopologue of the H- and D-containing pair, nine rotational transitions were accurately measured in the frequency region 88 GHz-1.2 THz. The analysis of the spectrum provided very precise rest frequencies at millimeter and sub-millimeter wavelengths, useful for the radioastronomical identification of the rotational lines of 15N2H+ and 15N2D+ in the ISM.

Optimized Shielding and Fabrication Techniques for TiN and Al Microwave Resonators

NASA Astrophysics Data System (ADS)

Kreikebaum, John Mark; Kim, Eunseong; Livingston, William; Dove, Allison; Calusine, Gregory; Hover, David; Rosenberg, Danna; Oliver, William; Siddiqi, Irfan

We present a systematic study of the effects of shielding and packaging on the internal quality factor (Qi) of Al and TiN microwave resonators designed for use in qubit readout. Surprisingly, Qi =1.3x106 TiN samples investigated at 100 mK exhibited no significant changes in linewidth when operated without magnetic shielding and in an open cryo-package. In contrast, Al resonators showed systematic improvement in Qi with each successive shield. Measurements were performed in an adiabatic demagnetization refrigerator, where typical ambient fields of 0.2 mT are present at the sample stage. We discuss the effect of 100 mK and 500 mK Cu radiation shields and cryoperm magnetic shielding on resonator Q as a function of temperature and input power in samples prepared with a variety of surface treatments, fabrication recipes, and embedding circuits. This research was supported by the ARO and IARPA.

Cross section measurement of 14N(p ,γ )15O in the CNO cycle

NASA Astrophysics Data System (ADS)

Li, Q.; Görres, J.; deBoer, R. J.; Imbriani, G.; Best, A.; Kontos, A.; LeBlanc, P. J.; Uberseder, E.; Wiescher, M.

2016-05-01

Background: The CNO cycle is the main energy source in stars more massive than our sun; it defines the energy production and the cycle time that lead to the lifetime of massive stars, and it is an important tool for the determination of the age of globular clusters. In our sun about 1.6% of the total solar neutrino flux comes from the CNO cycle. The largest uncertainty in the prediction of this CNO flux from the standard solar model comes from the uncertainty in the 14N(p ,γ )15O reaction rate; thus, the determination of the cross section at astrophysical temperatures is of great interest. Purpose: The total cross section of the 14N(p ,γ )15O reaction has large contributions from the transitions to the Ex=6.79 MeV excited state and the ground state of 15O. The Ex=6.79 MeV transition is dominated by radiative direct capture, while the ground state is a complex mixture of direct and resonance capture components and the interferences between them. Recent studies have concentrated on cross-section measurements at very low energies, but broad resonances at higher energy may also play a role. A single measurement has been made that covers a broad higher-energy range but it has large uncertainties stemming from uncorrected summing effects. Furthermore, the extrapolations of the cross section vary significantly depending on the data sets considered. Thus, new direct measurements have been made to improve the previous high-energy studies and to better constrain the extrapolation. Methods: Measurements were performed at the low-energy accelerator facilities of the nuclear science laboratory at the University of Notre Dame. The cross section was measured over the proton energy range from Ep=0.7 to 3.6 MeV for both the ground state and the Ex=6.79 MeV transitions at θlab=0∘ , 45∘, 90∘, 135∘, and 150∘. Both TiN and implanted-14N targets were utilized. γ rays were detected by using an array of high-purity germanium detectors. Results: The excitation function as

Site-specific 15N isotopic signatures of abiotically produced N2O

NASA Astrophysics Data System (ADS)

Heil, Jannis; Wolf, Benjamin; Brüggemann, Nicolas; Emmenegger, Lukas; Tuzson, Béla; Vereecken, Harry; Mohn, Joachim

2014-08-01

Efficient nitrous oxide (N2O) mitigation strategies require the identification of the main source and sink processes and their contribution to total soil N2O production. Several abiotic reactions of nitrification intermediates leading to N2O production are known, but their contribution to total N2O production in soils is uncertain. As the site preference (SP) of 15N in N2O is a promising tool to give more insight into N2O production processes, we investigated the SP of N2O produced by different abiotic reactions in a laboratory study. All reactions involved the nitrification intermediate hydroxylamine (NH2OH) in combination with nitrite (NO2-), Fe3+, Fe2+ and Cu2+, reactants commonly or potentially found in soils, at different concentrations and pH values. N2O production and its four main isotopic species (14N14N16O, 15N14N16O, 14N15N16O, and 14N14N18O) were quantified simultaneously and online at high temporal resolution using quantum cascade laser absorption spectroscopy. Thereby, our study presents the first continuous analysis of δ18O in N2O. The experiments revealed the possibility of purely abiotic reactions over a wide range of acidity (pH 3-8) by different mechanisms. All studied abiotic pathways produced N2O with a characteristic SP in the range of 34-35‰, unaffected by process conditions and remaining constant over the course of the experiments. These findings reflect the benefit of continuous N2O isotopic analysis by laser spectroscopy, contribute new information to the challenging source partitioning of N2O emissions from soils, and emphasize the potentially significant role of coupled biotic-abiotic reactions in soils.

Assignment Choice: Do Students Choose Briefer Assignments or Finishing What They Started?

ERIC Educational Resources Information Center

Hawthorn-Embree, Meredith L.; Skinner, Christopher H.; Parkhurst, John; O'Neil, Michael; Conley, Elisha

2010-01-01

Academic skill development requires engagement in effortful academic behaviors. Although students may be more likely to choose to engage in behaviors that require less effort, they also may be motivated to complete assignments that they have already begun. Seventh-grade students (N = 88) began a mathematics computation worksheet, but were stopped…

Resonance Raman Spectroscopy of Chirality Enriched Semiconducting Carbon Nanotubes

NASA Astrophysics Data System (ADS)

Hight Walker, A. R.; Piao, Y.; Simpson, J. R.; Lindsay, M.; Streit, J. K.; Ao, G.; Zheng, M.; Fagan, J. A.

Relative intensities of resonant Raman RBM and G modes of 11 chirality-enriched SWCNT species were established under second-order excitation. Results demonstrate an under-recognized complexity in evaluation of Raman spectra for assignment of (n,m) population distributions. Strong chiral angle and mod dependencies affect the intensity ratio of RBM/G modes and can result in misleading interpretations. We report 5 new (n,m) values for chirality-dependent G+ and G- Raman peak positions and intensity ratios, extending the available data to cover smaller diameters down to (5,4). The Raman spectral library sufficiently decouples G peaks from multiple species and enables fundamental characterization in mixed chirality samples. Our results on dispersive properties of the D modes will also be discussed. Probing defects is crucial to evaluate SWCNT quality and to understand the photophysics behind defect-induced optoelectronic features. Using high-quality, chirality-enriched semiconducting SWCNTs and tunable lasers, our results show a non-dispersive D band throughout the resonant window within the same (n,m). Our results were validated by multiple (n,m) samples and intentional covalent surface functionalization generating D peaks with increased intensity, which remain non-dispersive.

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

NASA Astrophysics Data System (ADS)

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 < 100.The coherent 15N enrichment in comets from different formation zones suggests that these isotopic enhancements are remnants of the interstellar chemistry in the 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

High-resolution NMR spectroscopic trends and assignment rules of metal-free, metallated and substituted corroles.

PubMed

Balazs, Yael S; Saltsman, Irena; Mahammed, Atif; Tkachenko, Elena; Golubkov, Galina; Levine, Joshua; Gross, Zeev

2004-07-01

Major advances over the last few years have facilitated the synthesis of a large variety of meso-only substituted corroles that display interesting catalytic, therapeutic and photophysical properties. This work is the first to study extensively the NMR spectral characteristics of both metallated and non-metallated triarylcorroles in various organic solvents and provide guidelines for easy and reliable assignments of 1D 1H spectra from trends of J coupling constants and chemical shifts. An excellent correlation is found between C=C bond lengths derived from 3J(H,H) values and experimental lengths determined by x-ray crystallography of the same molecules. The nuclear Overhauser effect provides a robust 1D 1H NMR tool for determining the selectivity of electrophilic substitutions. Variable-temperature NMR and isotopic labelling reveal a single preferred tautomerization state and unsymmetric ring orientations at -70 degrees C. The beta-pyrrole protons demonstrate long-range heteronuclear couplings with the coordination core (15N) and with the ortho-19F nuclei of the meso-carbon aryl rings. In sum, application of multinuclear magnetic resonance to corroles and their metal complexes, through the compilation of chemical shifts and J couplings and the recognition of trends therein, provides basic information essential to reliable spectral assignments. Additionally, the conclusions drawn about the structures of corroles and the electron densities at various positions of the corrole macrocycle resulting from the application of high-resolution NMR techniques are of importance to an in-depth understanding of the molecular interactions and processes of this relatively new and rapidly expanding class of compounds. Copyright 2004 John Wiley & Sons, Ltd.

Development of a Surface Plasmon Resonance n-dodecane Vapor Sensor

PubMed Central

Aguirre, Narcizo Muñoz; Pérez, Lilia Martínez; Colín, Jose Alfredo; Buenrostro-Gonzalez, Eduardo

2007-01-01

Using a high density polyethylene thin film over gold layer, a Surface Plasmon Resonance sensor for detecting n-dodecane vapor is developed. Preliminary results will be presented, showing that samples in the range of a few hundred ppm(V) of n-dodecane vapor in butane gas can be sensed. Also, studying the response as a function of time, it is demonstrated that the sensing process is quickly reversible. PMID:28903207

SUGGEL: A Program Suggesting the Orbital Angular Momentum of a Neutron Resonance from the Magnitude of its Neutron Width

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oh, S.Y.

2001-02-02

The SUGGEL computer code has been developed to suggest a value for the orbital angular momentum of a neutron resonance that is consistent with the magnitude of its neutron width. The suggestion is based on the probability that a resonance having a certain value of g{Gamma}{sub n} is an l-wave resonance. The probability is calculated by using Bayes' theorem on the conditional probability. The probability density functions (pdf's) of g{Gamma}{sub n} for up to d-wave (l=2) have been derived from the {chi}{sup 2} distribution of Porter and Thomas. The pdf's take two possible channel spins into account. This code ismore » a tool which evaluators will use to construct resonance parameters and help to assign resonance spin. The use of this tool is expected to reduce time and effort in the evaluation procedure, since the number of repeated runs of the fitting code (e.g., SAMMY) may be reduced.« less

Automated sequence-specific protein NMR assignment using the memetic algorithm MATCH.

PubMed

Volk, Jochen; Herrmann, Torsten; Wüthrich, Kurt

2008-07-01

MATCH (Memetic Algorithm and Combinatorial Optimization Heuristics) is a new memetic algorithm for automated sequence-specific polypeptide backbone NMR assignment of proteins. MATCH employs local optimization for tracing partial sequence-specific assignments within a global, population-based search environment, where the simultaneous application of local and global optimization heuristics guarantees high efficiency and robustness. MATCH thus makes combined use of the two predominant concepts in use for automated NMR assignment of proteins. Dynamic transition and inherent mutation are new techniques that enable automatic adaptation to variable quality of the experimental input data. The concept of dynamic transition is incorporated in all major building blocks of the algorithm, where it enables switching between local and global optimization heuristics at any time during the assignment process. Inherent mutation restricts the intrinsically required randomness of the evolutionary algorithm to those regions of the conformation space that are compatible with the experimental input data. Using intact and artificially deteriorated APSY-NMR input data of proteins, MATCH performed sequence-specific resonance assignment with high efficiency and robustness.

Fully automatic assignment of small molecules' NMR spectra without relying on chemical shift predictions.

PubMed

Castillo, Andrés M; Bernal, Andrés; Patiny, Luc; Wist, Julien

2015-08-01

We present a method for the automatic assignment of small molecules' NMR spectra. The method includes an automatic and novel self-consistent peak-picking routine that validates NMR peaks in each spectrum against peaks in the same or other spectra that are due to the same resonances. The auto-assignment routine used is based on branch-and-bound optimization and relies predominantly on integration and correlation data; chemical shift information may be included when available to fasten the search and shorten the list of viable assignments, but in most cases tested, it is not required in order to find the correct assignment. This automatic assignment method is implemented as a web-based tool that runs without any user input other than the acquired spectra. Copyright © 2015 John Wiley & Sons, Ltd.

Beam-Target Helicity Asymmetry for γ[over →]n[over →]→π^{-}p in the N^{*} Resonance Region.

PubMed

Ho, D; Peng, P; Bass, C; Collins, P; D'Angelo, A; Deur, A; Fleming, J; Hanretty, C; Kageya, T; Khandaker, M; Klein, F J; Klempt, E; Laine, V; Lowry, M M; Lu, H; Nepali, C; Nikonov, V A; O'Connell, T; Sandorfi, A M; Sarantsev, A V; Schumacher, R A; Strakovsky, I I; Švarc, A; Walford, N K; Wei, X; Whisnant, C S; Workman, R L; Zonta, I; Adhikari, K P; Adikaram, D; Akbar, Z; Amaryan, M J; Anefalos Pereira, S; Avakian, H; Ball, J; Bashkanov, M; Battaglieri, M; Batourine, V; Bedlinskiy, I; Biselli, A; Briscoe, W J; Burkert, V D; Carman, D S; Celentano, A; Charles, G; Chetry, T; Ciullo, G; Clark, L; Colaneri, L; Cole, P L; Contalbrigo, M; Crede, V; Dashyan, N; De Sanctis, E; De Vita, R; Djalali, C; Dupre, R; El Alaoui, A; El Fassi, L; Elouadrhiri, L; Eugenio, P; Fedotov, G; Fegan, S; Fersch, R; Filippi, A; Fradi, A; Ghandilyan, Y; Gilfoyle, G P; Girod, F X; Glazier, D I; Gleason, C; Gohn, W; Golovatch, E; Gothe, R W; Griffioen, K A; Guidal, M; Guo, L; Hakobyan, H; Harrison, N; Hattawy, M; Hicks, K; Holtrop, M; Hughes, S M; Ilieva, Y; Ireland, D G; Ishkhanov, B S; Isupov, E L; Jenkins, D; Jiang, H; Jo, H S; Joo, K; Joosten, S; Keller, D; Khachatryan, G; Kim, A; Kim, W; Klein, A; Kubarovsky, V; Kuleshov, S V; Lanza, L; Lenisa, P; Livingston, K; MacGregor, I J D; Markov, N; McKinnon, B; Mineeva, T; Mokeev, V; Montgomery, R A; Movsisyan, A; Munoz Camacho, C; Murdoch, G; Niccolai, S; Niculescu, G; Osipenko, M; Paolone, M; Paremuzyan, R; Park, K; Pasyuk, E; Phelps, W; Pogorelko, O; Price, J W; Procureur, S; Protopopescu, D; Ripani, M; Riser, D; Ritchie, B G; Rizzo, A; Rosner, G; Sabatié, F; Salgado, C; Sharabian, Y G; Skorodumina, Iu; Smith, G D; Sober, D I; Sokhan, D; Sparveris, N; Strauch, S; Tian, Ye; Torayev, B; Ungaro, M; Voskanyan, H; Voutier, E; Watts, D P; Wood, M H; Zachariou, N; Zhang, J; Zhao, Z W

2017-06-16

We report the first beam-target double-polarization asymmetries in the γ+n(p)→π^{-}+p(p) reaction spanning the nucleon resonance region from invariant mass W=1500 to 2300 MeV. Circularly polarized photons and longitudinally polarized deuterons in solid hydrogen deuteride (HD) have been used with the CEBAF Large Acceptance Spectrometer (CLAS) at Jefferson Lab. The exclusive final state has been extracted using three very different analyses that show excellent agreement, and these have been used to deduce the E polarization observable for an effective neutron target. These results have been incorporated into new partial wave analyses and have led to significant revisions for several γnN^{*} resonance photocouplings.

Compound-specific 15N analysis of amino acids in 15N tracer experiments provide an estimate of newly synthesised soil protein from inorganic and organic substrates

NASA Astrophysics Data System (ADS)

Charteris, Alice; Michaelides, Katerina; Evershed, Richard

2015-04-01

Organic N concentrations far exceed those of inorganic N in most soils and despite much investigation, the composition and cycling of this complex pool of SOM remains poorly understood. A particular problem has been separating more recalcitrant soil organic N from that actively cycling through the soil system; an important consideration in N cycling studies and for the soil's nutrient supplying capacity. The use of 15N-labelled substrates as stable isotope tracers has contributed much to our understanding of the soil system, but the complexity and heterogeneity of soil organic N prevents thorough compound-specific 15N analyses of organic N compounds and makes it difficult to examine any 15N-labelled organic products in any detail. As a result, a significant proportion of previous work has either simply assumed that since the majority of soil N is organic, all of the 15N retained in the soil is organic N (e.g. Sebilo et al., 2013) or subtracted 15N-labelled inorganic compounds from bulk values (e.g. Pilbeam et al., 1997). While the latter approach is more accurate, these methods only provide an estimate of the bulk 15N value of an extremely complex and non-uniformly labelled organic pool. A more detailed approach has been to use microbial biomass extraction (Brookes et al., 1985) and subsequent N isotopic analysis to determine the 15N value of biomass-N, representing the fraction of 15N assimilated by microbes or the 15N cycling through the 'living' or 'active' portion of soil organic N. However, this extraction method can only generate estimates and some lack of confidence in its validity and reliability remains. Here, we present an alternative technique to obtain a measure of the assimilation of an applied 15N substrate by the soil microbial biomass and an estimate of the newly synthesized soil protein, which is representative of the magnitude of the active soil microbial biomass. The technique uses a stable isotope tracer and compound-specific 15N analysis, but

47 CFR 90.723 - Selection and assignment of frequencies.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 47 Telecommunication 5 2011-10-01 2011-10-01 false Selection and assignment of frequencies. 90.723... 220-222 MHz Band § 90.723 Selection and assignment of frequencies. (a) Phase II applications for... systems, 10-channel EA systems, 15-channel Regional systems, public safety/mutual aid use, or emergency...

Compound-specific δ15N amino acid measurements in littoral mussels in the California upwelling ecosystem: a new approach to generating baseline δ15N Isoscapes for coastal ecosystems.

PubMed

Vokhshoori, Natasha L; McCarthy, Matthew D

2014-01-01

We explored δ(15)N compound-specific amino acid isotope data (CSI-AA) in filter-feeding intertidal mussels (Mytilus californianus) as a new approach to construct integrated isoscapes of coastal primary production. We examined spatial δ(15)N gradients in the California Upwelling Ecosystem (CUE), determining bulk δ(15)N values of mussel tissue from 28 sites between Port Orford, Oregon and La Jolla, California, and applying CSI-AA at selected sites to decouple trophic effects from isotopic values at the base of the food web. Bulk δ(15)N values showed a strong linear trend with latitude, increasing from North to South (from ∼ 7‰ to ∼ 12‰, R(2) = 0.759). In contrast, CSI-AA trophic position estimates showed no correlation with latitude. The δ(15)N trend is therefore most consistent with a baseline δ(15)N gradient, likely due to the mixing of two source waters: low δ(15)N nitrate from the southward flowing surface California Current, and the northward transport of the California Undercurrent (CUC), with (15)N-enriched nitrate. This interpretation is strongly supported by a similar linear gradient in δ(15)N values of phenylalanine (δ(15)NPhe), the best AA proxy for baseline δ(15)N values. We hypothesize δ(15)N(Phe) values in intertidal mussels can approximate annual integrated δ(15)N values of coastal phytoplankton primary production. We therefore used δ(15)N(Phe) values to generate the first compound-specific nitrogen isoscape for the coastal Northeast Pacific, which indicates a remarkably linear gradient in coastal primary production δ(15)N values. We propose that δ(15)N(Phe) isoscapes derived from filter feeders can directly characterize baseline δ(15)N values across major biochemical provinces, with potential applications for understanding migratory and feeding patterns of top predators, monitoring effects of climate change, and study of paleo- archives.

Sequence-specific 1H-NMR assignments for the aromatic region of several biologically active, monomeric insulins including native human insulin.

PubMed

Roy, M; Lee, R W; Kaarsholm, N C; Thøgersen, H; Brange, J; Dunn, M F

1990-06-12

The aromatic region of the 1H-FT-NMR spectrum of the biologically fully-potent, monomeric human insulin mutant, B9 Ser----Asp, B27 Thr----Glu has been investigated in D2O. At 1 to 5 mM concentrations, this mutant insulin is monomeric above pH 7.5. Coupling and amino acid classification of all aromatic signals is established via a combination of homonuclear one- and two-dimensional methods, including COSY, multiple quantum filters, selective spin decoupling and pH titrations. By comparisons with other insulin mutants and with chemically modified native insulins, all resonances in the aromatic region are given sequence-specific assignments without any reliance on the various crystal structures reported for insulin. These comparisons also give the sequence-specific assignments of most of the aromatic resonances of the mutant insulins B16 Tyr----Glu, B27 Thr----Glu and B25 Phe----Asp and the chemically modified species des-(B23-B30) insulin and monoiodo-Tyr A14 insulin. Chemical dispersion of the assigned resonances, ring current perturbations and comparisons at high pH have made possible the assignment of the aromatic resonances of human insulin, and these studies indicate that the major structural features of the human insulin monomer (including those critical to biological function) are also present in the monomeric mutant.

Interferometric Imaging of Titan’s HC3N, H13CCCN, and HCCC15N

NASA Astrophysics Data System (ADS)

Cordiner, M. A.; Nixon, C. A.; Charnley, S. B.; Teanby, N. A.; Molter, E. M.; Kisiel, Z.; Vuitton, V.

2018-05-01

We present the first maps of cyanoacetylene isotopologues in Titan’s atmosphere, including H13CCCN and HCCC15N, detected in the 0.9 mm band using the Atacama Large Millimeter/submillimeter array (ALMA) around the time of Titan’s (southern winter) solstice in 2017 May. The first high-resolution map of HC3N in its v 7 = 1 vibrationally excited state is also presented, revealing a unique snapshot of the global HC3N distribution, free from the strong optical depth effects that adversely impact the ground-state (v = 0) map. The HC3N emission is found to be strongly enhanced over Titan’s south pole (by a factor of 5.7 compared to the north pole), consistent with rapid photochemical loss of HC3N from the summer hemisphere combined with production and transport to the winter pole since the 2015 April ALMA observations. The H13CCCN/HCCC15N flux ratio is derived at the southern HC3N peak, and implies an HC3N/HCCC15N ratio of 67 ± 14. This represents a significant enrichment in 15N compared with Titan’s main molecular nitrogen reservoir, which has a 14N/15N ratio of 167, and confirms the importance of photochemistry in determining the nitrogen isotopic ratio in Titan’s organic inventory.

Solution structure of the DNA-binding domain of the heat shock transcription factor determined by multidimensional heteronuclear magnetic resonance spectroscopy.

PubMed Central

Damberger, F. F.; Pelton, J. G.; Harrison, C. J.; Nelson, H. C.; Wemmer, D. E.

1994-01-01

The solution structure of the 92-residue DNA-binding domain of the heat shock transcription factor from Kluyveromyces lactis has been determined using multidimensional NMR methods. Three-dimensional (3D) triple resonance, 1H-13C-13C-1H total correlation spectroscopy, and 15N-separated total correlation spectroscopy-heteronuclear multiple quantum correlation experiments were used along with various 2D spectra to make nearly complete assignments for the backbone and side-chain 1H, 15N, and 13C resonances. Five-hundred eighty-three NOE constraints identified in 3D 13C- and 15N-separated NOE spectroscopy (NOESY)-heteronuclear multiple quantum correlation spectra and a 4-dimensional 13C/13C-edited NOESY spectrum, along with 35 phi, 9 chi 1, and 30 hydrogen bond constraints, were used to calculate 30 structures by hybrid distance geometry/stimulated annealing protocol, of which 24 were used for structural comparison. The calculations revealed that a 3-helix bundle packs against a small 4-stranded antiparallel beta-sheet. The backbone RMS deviation (RMSD) for the family of structures was 1.03 +/- 0.19 A with respect to the average structure. The topology is analogous to that of the C-terminal domain of the catabolite gene activator protein and appears to be in the helix-turn-helix family of DNA-binding proteins. The overall fold determined by the NMR data is consistent with recent crystallographic work on this domain (Harrison CJ, Bohm AA, Nelson HCM, 1994, Science 263:224) as evidenced by RMSD between backbone atoms in the NMR and X-ray structures of 1.77 +/- 0.20 A. Several differences were identified some of which may be due to protein-protein interactions in the crystal. PMID:7849597

Chemical shift assignments of the first and second RRMs of Nrd1, a fission yeast MAPK-target RNA binding protein.

PubMed

Kobayashi, Ayaho; Kanaba, Teppei; Satoh, Ryosuke; Ito, Yutaka; Sugiura, Reiko; Mishima, Masaki

2017-10-01

Negative regulator differentiation 1 (Nrd1), a fission yeast RNA binding protein, modulates cytokinesis and sexual development and contributes to stress granule formation in response to environmental stresses. Nrd1 comprises four RRM domains and binds and stabilizes Cdc4 mRNA that encodes the myosin II light chain. Nrd1 binds the Cpc2 fission-yeast RACK1 homolog, and the interaction promotes Nrd1 localization to stress granules. Interestingly, Pmk1 mitogen-activated protein kinase phosphorylates Thr40 in the unstructured N-terminal region and Thr126 in the first RRM domain of Nrd1. Phosphorylation significantly reduces RNA-binding activity and likely modulates Nrd1 function. To reveal the relationship between the structure and function of Nrd1 and how phosphorylation affects structure, we used heteronuclear NMR techniques to investigate the three-dimensional structure of Nrd1. Here we report the 1 H, 13 C, and 15 N resonance assignments of RRM1-RRM2 (residues 108-284) comprising the first and second RRMs obtained using heteronuclear NMR techniques. Secondary structures derived from the chemical shifts are reported. These data should contribute to the understanding of the three-dimensional structure of the RRM1-RRM2 region of Nrd1 and the perturbation caused by phosphorylation.

Ammonia 15N/14N Isotope Ratio in the Jovian Atmosphere

NASA Technical Reports Server (NTRS)

Mahaffy, P.R.; Niemann, H. B.; Atreya, S. K.; Wong, M. H.; Owen, T. C; Einaudi, Franco (Technical Monitor)

2000-01-01

Data from the Galileo Probe Mass Spectrometer has been used to derive the N-15/N-14 isotope ratio in ammonia at Jupiter. Although the mass spectral interference from the water contribution to 18 amu makes an accurate derivation of the (N-15)H3/(N-14)H3 ratio difficult from measurements of the singly ionized signals at 18 and 17 amu, this interference is not present in the doubly charged 8.5 and 9.0 amu signals from (N-14)H3++ and (N-15)H3++ respectively. Although the count rate from the 9 amu signal is low during the direct sampling of the atmosphere, the ammonia signal was considerably enhanced during the first enrichment cell (EC1) experiment that measured gas sampled between 0.8 and 2.8 bar. Count rates at 9 amu in the EC1 experiment reach 60/second and measure ammonia sampled from 0.88 to 2.8 bar. In the EC1 measurements the 8.5 amu signal is not measured directly, but can be calculated from the ammonia contribution to 17 amu and the ratio of NH3 ions of a double to single charged observed during a high resolution mass scan taken near the end of the descent. The high resolution scan gives this ratio from ammonia sampled much deeper in the atmosphere. These results are described and compared with Infrared Space Observatory-Short Wavelength Spectrometer (ISO-SWS) observations that give this ratio at 400 mbar.

Scissors Mode of 162 Dy Studied from Resonance Neutron Capture

DOE PAGES

Baramsai, B.; Bečvář, F.; Bredeweg, T. A.; ...

2015-05-28

Multi-step cascade γ-ray spectra from the neutron capture at isolated resonances of 161Dy nucleus were measured at the LANSCE/DANCE time-of-flight facility in Los Alamos National Laboratory. The objectives of this experiment were to confirm and possibly extend the spin assignment of s-wave neutron resonances and get new information on photon strength functions with emphasis on the role of the M1 scissors mode vibration. The preliminary results show that the scissors mode plays a significant role in all transitions between accessible states of the studied nucleus. The photon strength functions describing well our data are compared to results from 3He-induced reactions,more » (n,γ) experiments on Gd isotopes, and (γ,γ’) reactions.« less

Selective p-i-n photodetector with resonant tunneling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mil'shtein, S.; Wilson, S.; Pillai, A.

2014-05-15

There are different fundamental approaches to designing selective photodetectors, where the selectivity of optical spectra is produced by a filtering aperture. However, manufacturing of multilayered filters is cumbersome for epitaxial technology. In the current study, we offer a novel approach in design of selective photodetectors. A p-i-n photodetector with superlattices in top n-layer becomes transparent for photons where hν<>E{sub ng}+E{sub n1}, the light will be absorbed, simultaneously producing high energy (hot) electrons. The designed thickness of the structure does prevent thermal relaxation of high energy electrons by thus enhancing the selectivity of the photodetector. However the most important selectivity elementmore » is the resonant tunneling which does happen only for electrons occupying E{sub n1} energy levels as they transfer to levels E{sub i1}aligned under reverse biasing.« less

206Pb+n resonances for E=600-900 keV: Neutron strength functions

NASA Astrophysics Data System (ADS)

Horen, D. J.; Harvey, J. A.; Hill, N. W.

1981-11-01

Data from high resolution neutron transmission and differential scattering measurements performed on 206Pb have been analyzed for E=600-900 keV. Resonance parameters (i.e., E, l, J, and Γn) have been deduced for many of the 161 resonances observed. Strength functions and potential phase shifts for s-, p-, and d-wave neutrons for En-0-900 keV are compared with optical model calculations. It is found that the phase contributed by the external R function as well as the integrated neutron strength functions can be reproduced for the s and d waves with a well depth of V0=50.4 MeV for the real potential and WD=6.0 MeV for an imaginary surface potential. Somewhat smaller values (V0=48.7 MeV and WD=2.0 MeV) are required to reproduce the p-wave data. These values of the real potential are also found to give the experimentally observed binding energies for the 4s12, 3d32, and 3d52 single particle levels (V0=50.4 MeV), and the 3p12 single particle level (V0=48.7 MeV). Nuclear level densities for s and d waves are found to be well represented by a constant temperature model. However, the model under estimates the number of p-wave resonances. NUCLEAR REACTIONS 206Pb(n), (n,n), E=600-900 keV; measured σT(E), σ(E,θ). 207Pb deduced resonance parameters, Jπ, Γn, neutron strength functions, optical model parameters for l=0,1,2.

Deuterium and 15N fractionation in N2H+ during the formation of a Sun-like star

NASA Astrophysics Data System (ADS)

De Simone, M.; Fontani, F.; Codella, C.; Ceccarelli, C.; Lefloch, B.; Bachiller, R.; López-Sepulcre, A.; Caux, E.; Vastel, C.; Soldateschi, J.

2018-05-01

Although chemical models predict that the deuterium fractionation in N2H+ is a good evolutionary tracer in the star formation process, the fractionation of nitrogen is still a poorly understood process. Recent models have questioned the similar evolutionary trend expected for the two fractionation mechanisms in N2H+, based on a classical scenario in which ion-neutral reactions occurring in cold gas should have caused an enhancement of the abundance of N2D+, 15NNH+, and N15NH+. In the framework of the ASAI IRAM-30m large program, we have investigated the fractionation of deuterium and 15N in N2H+ in the best known representatives of the different evolutionary stages of the Sun-like star formation process. The goal is to ultimately confirm (or deny) the classical `ion-neutral reactions' scenario that predicts a similar trend for D and 15N fractionation. We do not find any evolutionary trend of the 14N/15N ratio from both the 15NNH+ and N15NH+ isotopologues. Therefore, our findings confirm that, during the formation of a Sun-like star, the core evolution is irrelevant in the fractionation of 15N. The independence of the 14N/15N ratio with time, found also in high-mass star-forming cores, indicates that the enrichment in 15N revealed in comets and protoplanetary discs is unlikely to happen at core scales. Nevertheless, we have firmly confirmed the evolutionary trend expected for the H/D ratio, with the N2H+/N2D+ ratio decreasing before the pre-stellar core phase, and increasing monotonically during the protostellar phase. We have also confirmed clearly that the two fractionation mechanisms are not related.

Regional assessment of N saturation using foliar and root δ15N

Treesearch

L.H. Pardo; P.H. Templer; C.L. Goodale; S. Duke; P.M. Groffman; M.B. Adams; P. Boeckx; J. Boggs; J. Campbell; B. Colman; J. Compton; B. Emmett; P. Gundersen; J. Kjonaas; G. Lovett; M. Mack; A. Magill; M. Mbila; M.J. Mitchell; G. McGee; S. McNulty; K. Nadelhoffer; S. Ollinger; D. Ross; H. Rueth; L. Rustad; P. Schaberg; S. Schiff; P. Schleppi; J. Spoelstra; W. Wessel

2006-01-01

N saturation induced by atmospheric N deposition can have serious consequences for forest health in many regions. In order to evaluate whether foliar δ15N may be a robust, regional-scale measure of the onset of N saturation in forest ecosystems, we assembled a large dataset on atmospheric N deposition, foliar and root δ

The first science result with the JENSA gas-jet target: Confirmation and study of a strong subthreshold F 18 ( p , α ) O 15 resonance

DOE PAGES

Bardayan, D. W.; Chipps, K. A.; Ahn, S.; ...

2015-11-28

The astrophysical 18F( p,α) 15O rate determines, in large part, the extent to which the observable radioisotope 18F is produced in novae. This rate, however, has been extremely uncertain owing to the unknown properties of a strong subthreshold resonance and its possible interference with higher-lying resonances. In addition, the new Jet Experiments in Nuclear Structure and Astrophysics (JENSA) gas-jet target has been used for the first time to determine the spin of this important resonance and significantly reduce uncertainties in the 18F( p,α) 15O rate.

The first science result with the JENSA gas-jet target: Confirmation and study of a strong subthreshold F 18 ( p , α ) O 15 resonance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bardayan, D. W.; Chipps, K. A.; Ahn, S.

The astrophysical 18F( p,α) 15O rate determines, in large part, the extent to which the observable radioisotope 18F is produced in novae. This rate, however, has been extremely uncertain owing to the unknown properties of a strong subthreshold resonance and its possible interference with higher-lying resonances. In addition, the new Jet Experiments in Nuclear Structure and Astrophysics (JENSA) gas-jet target has been used for the first time to determine the spin of this important resonance and significantly reduce uncertainties in the 18F( p,α) 15O rate.

Negotiating Assignment Pathways: Students and Academic Assignments

ERIC Educational Resources Information Center

McDowell, Liz

2008-01-01

Existing research identifies that students' approaches to assignments are related to their general approaches to study. It is suggested that students need to better understand the requirements of assignments and acquire new concepts such as "argument". This fine-grained study proposes four qualitatively distinct assignment pathways: gathering,…

First Measurements of 15N Fractionation in N2H+ toward High-mass Star-forming Cores

NASA Astrophysics Data System (ADS)

Fontani, F.; Caselli, P.; Palau, A.; Bizzocchi, L.; Ceccarelli, C.

2015-08-01

We report on the first measurements of the isotopic ratio 14N/15N in N2H+ toward a statistically significant sample of high-mass star-forming cores. The sources belong to the three main evolutionary categories of the high-mass star formation process: high-mass starless cores, high-mass protostellar objects, and ultracompact H ii regions. Simultaneous measurements of the 14N/15N ratio in CN have been made. The 14N/15N ratios derived from N2H+ show a large spread (from ∼180 up to ∼1300), while those derived from CN are in between the value measured in the terrestrial atmosphere (∼270) and that of the proto-solar nebula (∼440) for the large majority of the sources within the errors. However, this different spread might be due to the fact that the sources detected in the N2H+ isotopologues are more than those detected in the CN ones. The 14N/15N ratio does not change significantly with the source evolutionary stage, which indicates that time seems to be irrelevant for the fractionation of nitrogen. We also find a possible anticorrelation between the 14N/15N (as derived from N2H+) and the H/D isotopic ratios. This suggests that 15N enrichment could not be linked to the parameters that cause D enrichment, in agreement with the prediction by recent chemical models. These models, however, are not able to reproduce the observed large spread in 14N/15N, pointing out that some important routes of nitrogen fractionation could be still missing in the models. Based on observations carried out with the IRAM-30 m Telescope. IRAM is supported by INSU/CNRS (France), MPG (Germany), and IGN (Spain).

(13)C and (15)N solid-state NMR studies on albendazole and cyclodextrin albendazole complexes.

PubMed

Ferreira, M João G; García, A; Leonardi, D; Salomon, Claudio J; Lamas, M Celina; Nunes, Teresa G

2015-06-05

(13)C and (15)N solid-state nuclear magnetic resonance (NMR) spectra were recorded from albendazole (ABZ) and from ABZ:β-cyclodextrin, ABZ:methyl-β-cyclodextrin, ABZ:hydroxypropyl-β-cyclodextrin and ABZ:citrate-β-cyclodextrin, which were prepared by the spray-drying technique. ABZ signals were typical of a crystalline solid for the pure drug and of an amorphous compound obtained from ABZ:cyclodextrin samples. Relevant spectral differences were correlated with chemical interaction between ABZ and cyclodextrins. The number and type of complexes revealed a strong dependence on the cyclodextrin group substituent. Solid-state NMR data were consistent with the presence of stable inclusion complexes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Complete Measurement of Stable Isotopes in N2O (δ15N, δ15Nα, δ15Nβ, δ18O, δ17O) Using Off-Axis Integrated Cavity Output Spectroscopy (OA-ICOS)

NASA Astrophysics Data System (ADS)

Leen, J. B.; Gupta, M.

2014-12-01

Nitrate contamination in water is a worldwide environmental problem and source apportionment is critical to managing nitrate pollution. Fractionation caused by physical, chemical and biological processes alters the isotope ratios of nitrates (15N/14N, 18O/16O and 17O/16O) and biochemical nitrification and denitrification impart different intramolecular site preference (15N14NO vs. 14N15NO). Additionally, atmospheric nitrate is anomalously enriched in 17O compared to other nitrate sources. The anomaly (Δ17O) is conserved during fractionation processes, providing a tracer of atmospheric nitrate. All of these effects can be used to apportion nitrate in soil. Current technology for measuring nitrate isotopes is complicated and costly - it involves conversion of nitrate to nitrous oxide (N2O), purification, preconcentration and measurement by isotope ratio mass spectrometer (IRMS). Site specific measurements require a custom IRMS. There is a pressing need to make this measurement simpler and more accessible. Los Gatos Research has developed a next generation mid-infrared Off-Axis Integrated Cavity Output Spectroscopy (OA-ICOS) analyzer to quantify all stable isotope ratios of N2O (δ15N, δ15Nα, δ15Nβ, δ18O, δ17O). We present the latest performance data demonstrating the precision and accuracy of the OA-ICOS based measurement. At an N2O concentration of 322 ppb, the analyzer quantifies [N2O], δ15N, δ15Na, δ15Nb, and δ18O with a precision of ±0.05 ppb, ±0.4 ‰, ±0.45 ‰, and ±0.6 ‰, and ±0.8 ‰ respectively (1σ, 100s; 1σ, 1000s for δ18O). Measurements of gas standards demonstrate accuracy better than ±1 ‰ for isotope ratios over a wide dynamic range (200 - 100,000 ppb). The measurement of δ17O requires a higher concentration (1 - 50 ppm), easily obtainable through conversion of nitrates in water. For 10 ppm of N2O, the instrument achieves a δ17O precision of ±0.05 ‰ (1σ, 1000s). This performance is sufficient to quantify atmospheric

Observation of resonant and non-resonant magnetic braking in the n = 1 non-axisymmetric configurations on KSTAR

NASA Astrophysics Data System (ADS)

Kim, Kimin; Choe, W.; In, Y.; Ko, W. H.; Choi, M. J.; Bak, J. G.; Kim, H. S.; Jeon, Y. M.; Kwak, J. G.; Yoon, S. W.; Oh, Y. K.; Park, J.-K.

2017-12-01

Toroidal rotation braking by neoclassical toroidal viscosity driven by non-axisymmetric (3D) magnetic fields, called magnetic braking, has great potential to control rotation profile, and thereby modify tokamak stability and performance. In order to characterize magnetic braking in the various 3D field configurations, dedicated experiments have been carried out in KSTAR, applying a variety of static n=1 , 3D fields of different phasing of -90 , 0, and +90 . Resonant-type magnetic braking was achieved by -90 phasing fields, accompanied by strong density pump-out and confinement degradation, and explained by excitation of kink response captured by ideal plasma response calculation. Strong resonant plasma response was also observed under +90 phasing at q95 ∼ 6 , leading to severe confinement degradation and eventual disruption by locked modes. Such a strong resonant transport was substantially modified to non-resonant-type transport at higher q95 ∼ 7.2 , as the resonant particle transport was significantly reduced and the rotation braking was pushed to plasma edge. This is well explained by ideal perturbed equilibrium calculations indicating the strong kink coupling at lower q95 is reduced at higher q95 discharge. The 0 phasing fields achieved quiescent magnetic braking without density pump-out and confinement degradation, which is consistent with vacuum and ideal plasma response analysis predicting deeply penetrating 3D fields without an excitation of strong kink response.

Astrophysical S factor for the {sup 15}N(p,{gamma}){sup 16}O reaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mukhamedzhanov, A. M.; La Cognata, M.; Kroha, V.

2011-04-15

The R-matrix approach has proved to be very useful in extrapolating the astrophysical factor down to astrophysically relevant energies, since the majority of measurements are not available in this region. However, such an approach has to be critically considered when no complete knowledge of the reaction model is available. To get reliable results in such cases one has to use all the available information from independent sources and, accordingly, fix or constrain variations of the parameters. In this paper we present a thorough R-matrix analysis of the {sup 15}N(p,{gamma}){sup 16}O reaction, which provides a path from the CN cycle tomore » the CNO bi-cycle and CNO tri-cycle. The measured astrophysical factor for this reaction is dominated by resonant capture through two strong J{sup {pi}}=1{sup -} resonances at E{sub R}=312 and 962 keV and direct capture to the ground state. Recently, a new measurement of the astrophysical factor for the {sup 15}N(p,{gamma}){sup 16}O reaction has been published [P. J. LeBlanc et al., Phys. Rev. C 82, 055804 (2010)]. The analysis has been done using the R-matrix approach with unconstrained variation of all parameters including the asymptotic normalization coefficient (ANC). The best fit has been obtained for the square of the ANC C{sup 2}=539.2 fm{sup -1}, which exceeds the previously measured value by a factor of {approx_equal}3. Here we present a new R-matrix analysis of the Notre Dame-LUNA data with the fixed within the experimental uncertainties square of the ANC C{sup 2}=200.34 fm{sup -1}. Rather than varying the ANC we add the contribution from a background resonance that effectively takes into account contributions from higher levels. Altogether we present ten fits, seven unconstrained and three constrained. For the unconstrained fit with the boundary condition B{sub c}=S{sub c}(E{sub 2}), where E{sub 2} is the energy of the second level, we get S(0)=39.0{+-}1.1 keVb and normalized {chi}-tilde{sup 2}=1.84, i.e., the result

Using Hyperfine Electron Paramagnetic Resonance Spectroscopy to Define the Proton-Coupled Electron Transfer Reaction at Fe-S Cluster N2 in Respiratory Complex I.

PubMed

Le Breton, Nolwenn; Wright, John J; Jones, Andrew J Y; Salvadori, Enrico; Bridges, Hannah R; Hirst, Judy; Roessler, Maxie M

2017-11-15

Energy-transducing respiratory complex I (NADH:ubiquinone oxidoreductase) is one of the largest and most complicated enzymes in mammalian cells. Here, we used hyperfine electron paramagnetic resonance (EPR) spectroscopic methods, combined with site-directed mutagenesis, to determine the mechanism of a single proton-coupled electron transfer reaction at one of eight iron-sulfur clusters in complex I, [4Fe-4S] cluster N2. N2 is the terminal cluster of the enzyme's intramolecular electron-transfer chain and the electron donor to ubiquinone. Because of its position and pH-dependent reduction potential, N2 has long been considered a candidate for the elusive "energy-coupling" site in complex I at which energy generated by the redox reaction is used to initiate proton translocation. Here, we used hyperfine sublevel correlation (HYSCORE) spectroscopy, including relaxation-filtered hyperfine and single-matched resonance transfer (SMART) HYSCORE, to detect two weakly coupled exchangeable protons near N2. We assign the larger coupling with A( 1 H) = [-3.0, -3.0, 8.7] MHz to the exchangeable proton of a conserved histidine and conclude that the histidine is hydrogen-bonded to N2, tuning its reduction potential. The histidine protonation state responds to the cluster oxidation state, but the two are not coupled sufficiently strongly to catalyze a stoichiometric and efficient energy transduction reaction. We thus exclude cluster N2, despite its proton-coupled electron transfer chemistry, as the energy-coupling site in complex I. Our work demonstrates the capability of pulse EPR methods for providing detailed information on the properties of individual protons in even the most challenging of energy-converting enzymes.

Sum-over-states density functional perturbation theory: Prediction of reliable 13C, 15N, and 17O nuclear magnetic resonance chemical shifts

NASA Astrophysics Data System (ADS)

Olsson, Lars; Cremer, Dieter

1996-11-01

Sum-over-states density functional perturbation theory (SOS-DFPT) has been used to calculate 13C, 15N, and 17O NMR chemical shifts of 20 molecules, for which accurate experimental gas-phase values are available. Compared to Hartree-Fock (HF), SOS-DFPT leads to improved chemical shift values and approaches the degree of accuracy obtained with second order Møller-Plesset perturbation theory (MP2). This is particularly true in the case of 15N chemical shifts where SOS-DFPT performs even better than MP2. Additional improvements of SOS-DFPT chemical shifts can be obtained by empirically correcting diamagnetic and paramagnetic contributions to compensate for deficiencies which are typical of DFT.

Sewage derive [sup 15]N in the Baltic traced in fucus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hobbie, J.E.; Fry, B.; Larsson, U.

Himmerfjarden, a fjord-like bay on the eastern shore of the Baltic, receives treated sewage from 250,000 inhabitants. Because the inorganic N in the effluent is enriched in [sup 15]N through denitrification, nitrification, and ammonia volatilization, an analysis of the distribution of [sup 15]N in the Bay tells how far from the source the sewage nitrogen moves. The attached macroalga Fucus vesiculosus was collected in early May from rocky shore at 0-0.5 m depth and the [sup 15]N content of the tips of the fronds analyzed. This N represents uptake and storage during the previous six months and growth during Marchmore » and April. The [delta][sup 15]N was uniformly high (11-13[per thousand]) in the main body of the Bay within 15 km from the sewage source. Beyond 15 km values decreased with distance to a low of 4.6[per thousand] at 35 km, where the Bay ends and the coastal waters begin. Using the 11-13 and 4.6[per thousand] as endmembers, the percentage of sewage N making up the Fucus at any point may be calculated. The [delta][sub 15]N of particulate organic matter in the offshore Baltic waters was around 0[per thousand] and Fucus had an [delta][sup 15]N about 1.5[per thousand] higher than the POM. From this and other evidence we conclude that there is a belt of coastal water with an elevated [delta][sup 15]N lying along the east coast of the Baltic. This presumably derives from sewage and perhaps from agriculture and is potentially of use as a tracer of coastal zone/pelagic zone interactions.« less

[Dynamics of amino acid and protein metabolism of laying hens after administration of 15N-labeled wheat protein. 5. Incorporation of 15N into the blood fraction and its amino acids].

PubMed

Gruhn, K; Zander, R; Kirchner, E

1987-09-01

12 colostomized laying hens which received 15N labelled wheat over 4 days were butchered 12 h, 36 h, 60 h and 108 h (3 animals each) after the last 15N application. The intake of 15N excess (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 trichloric acetic 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.

A study of spin isovector giant resonances with the208Pb(n, p)208Tl reaction

NASA Astrophysics Data System (ADS)

Moinester, M. A.; Trudel, A.; Raywood, K.; Yen, S.; Spicer, B. M.; Abegg, R.; Alford, W. P.; Auerbach, N.; Celler, A.; Frekers, D.; Häusser, O.; Helmer, R. L.; Henderson, R.; Hicks, K. H.; Jackson, K. P.; Jeppesen, R. G.; King, N. S. P.; Long, S.; Miller, C. A.; Vetterli, M.; Watson, J.; Yavin, A. I.

1989-10-01

The208Pb(n, p)208Tl reaction was studied at 198 and 458 MeV in a search for isovector spin giant resonances. Peaks at 5.1 MeV and 13.6 MeV excitation in208Tl are observed and discussed as candidates for the T> spin giant dipole resonance (SGDR), the spin isovector monopole resonance (SIVM), and the spin isovector quadrupole resonance (SIVQ).

Nitrogen stable isotope composition (δ15N) of vehicle-emitted NOx.

PubMed

Walters, Wendell W; Goodwin, Stanford R; Michalski, Greg

2015-02-17

The nitrogen stable isotope ratio of NOx (δ(15)N-NOx) has been proposed as a regional indicator for NOx source partitioning; however, knowledge of δ(15)N values from various NOx emission sources is limited. This study presents a detailed analysis of δ(15)N-NOx emitted from vehicle exhaust, the largest source of anthropogenic NOx. To accomplish this, NOx was collected from 26 different vehicles, including gasoline and diesel-powered engines, using a modification of a NOx collection method used by the United States Environmental Protection Agency, and δ(15)N-NOx was analyzed. The vehicles sampled in this study emitted δ(15)N-NOx values ranging from -19.1 to 9.8‰ that negatively correlated with the emitted NOx concentrations (8.5 to 286 ppm) and vehicle run time because of kinetic isotope fractionation effects associated with the catalytic reduction of NOx. A model for determining the mass-weighted δ(15)N-NOx from vehicle exhaust was constructed on the basis of average commute times, and the model estimates an average value of -2.5 ± 1.5‰, with slight regional variations. As technology improvements in catalytic converters reduce cold-start emissions in the future, it is likely to increase current δ(15)N-NOx values emitted from vehicles.

Enchancement of the Ionosphere Alfvén Resonance caused by earthquake: experiment and model

NASA Astrophysics Data System (ADS)

Kotsarenko, A.; Grimalsky, V.; Pulinets, S.; Koshevaya, S.; Perez-Enriquez, R.; Cruz Abeyro, J. A. L.

2009-04-01

Analysis of geomagnetic and telluric data, measured at the station PRK (Parkfield, ULF flux-gate 3-axial magnetometer) 1 week before (including) the day of major EQ (EarthQuake, Ms=6.0, 28-SEP-2004, 17:15:24) near Parkfield, California, USA, are presented. Spectral analysis reveals enhancement the IAR (Ionosphere Alfvén Resonance) modes, localized in the frequency range 0.25-1 Hz, observed the day before the event, Sep 27, at 15:00-20:00 by UT, and at the day of the EQ, Sep 28, at 11:00-19:00 (9 hours before the event). Estimations of the amplitudes of the signals give following values: up to 20 pT for the magnetic channels and 1.5 mkV/km for the telluric ones. Observed phenomena occurs under quiet geomagnetic conditions (|Dst|< 20 nT). We have calculated the efficiency of the modulation of the Alfvén wave at frequencies f = 0.1 - 10 Hz, which passes from the magnetosphere (z > 600 km) to the ionosphere and the to the Earth's surface and the lithosphere. The set of equations for the both magnetic and electric field components has been solved numerically. It has been obtained that the 20% modulation of the concentration of the ion and electron concentrations (which is also observed experimentally) at the heights z = 200 km can lead to the same (or higher) modulation of the amplitude of the variable magnetic field at the Earth's surface (z = 0) at f = 0.1 - 10 Hz. Moreover, the effect depends weakly on the conductivity of the lithosphere. Therefore, an influence of the coupling mechanisms on the F-layer of the ionosphere could lead to observable effects at the Earth's surface.

Discrimination of benign and malignant lymph nodes at 7.0T compared to 1.5T magnetic resonance imaging using ultrasmall particles of iron oxide: a feasibility preclinical study.

PubMed

Kinner, Sonja; Maderwald, Stefan; Albert, Juliane; Parohl, Nina; Corot, Claire; Robert, Philippe; Baba, Hideo A; Barkhausen, Jörg

2013-12-01

To investigate the feasibility and performance of 7T magnetic resonance imaging compared to 1.5T imaging to discriminate benign (normal and inflammatory changed) from tumor-bearing lymph nodes in rabbits using ultrasmall particles of iron oxide (USPIO)-based contrast agents. Six New Zealand White rabbits were inoculated with either complete Freund's adjuvant cell suspension (n = 3) to induce reactively enlarged lymph nodes or with VX2 tumor cells to produce metastatic lymph nodes (n = 3). Image acquisition was performed before and 24 hours after bolus injection of an USPIO contrast agent at 1.5T and afterward at 7T using T1-weighted and T2*-weighted sequences. Sensitivities, specificities, and negative and positive predictive values for the detection of lymph node metastases were calculated for both field strengths with histopathology serving as reference standard. Sizes of lymph nodes with no, inflammatory, and malignant changes were compared using a Mann-Whitney U-test. All 24 lymph nodes were detected at 1.5T as well as at 7T. At 1.5T, sensitivity amounted to 0.67, while specificity reached a value of 1. At the higher field strength (7T), imaging was able to reach sensitivity and specificity values of 1. No statistical differences were detected concerning lymph node sizes. Magnetic resonance lymphography with USPIO contrast agents allows for differentiation of normal and reactively enlarged lymph nodes compared to metastatic nodes. First experiments at 7T show promising results compared to 1.5T, which have to be evaluated in further trials. Copyright © 2013. Published by Elsevier Inc.

Ionospheric Alfvén resonator and aurora: Modeling of MICA observations

NASA Astrophysics Data System (ADS)

Tulegenov, B.; Streltsov, A. V.

2017-07-01

We present results from a numerical study of small-scale, intense magnetic field-aligned currents observed in the vicinity of the discrete auroral arc by the Magnetosphere-Ionosphere Coupling in the Alfvén Resonator (MICA) sounding rocket launched from Poker Flat, Alaska, on 19 February 2012. The goal of the MICA project was to investigate the hypothesis that such currents can be produced inside the ionospheric Alfvén resonator by the ionospheric feedback instability (IFI) driven by the system of large-scale magnetic field-aligned currents interacting with the ionosphere. The trajectory of the MICA rocket crossed two discrete auroral arcs and detected packages of intense, small-scale currents at the edges of these arcs, in the most favorable location for the development of the ionospheric feedback instability, predicted by the IFI theory. Simulations of the reduced MHD model derived in the dipole magnetic field geometry with realistic background parameters confirm that IFI indeed generates small-scale ULF waves inside the ionospheric Alfvén resonator with frequency, scale size, and amplitude showing a good, quantitative agreement with the observations. The comparison between numerical results and observations was performed by "flying" a virtual MICA rocket through the computational domain, and this comparison shows that, for example, the waves generated in the numerical model have frequencies in the range from 0.30 to 0.45 Hz, and the waves detected by the MICA rocket have frequencies in the range from 0.18 to 0.50 Hz.

H6+ in irradiated solid para-hydrogen and its decay dynamics: reinvestigation of quartet electron paramagnetic resonance lines assigned to H2-.

PubMed

Kumada, Takayuki; Tachikawa, Hiroto; Takayanagi, Toshiyuki

2005-03-07

The quartet electron paramagnetic resonance (EPR) lines observed in gamma- and X-ray irradiated solid para-H2, which have previously been assigned to H2-, are reinvestigated. We have reassigned the quartet lines to H6 rather than H2- mainly due to comparison of experimentally obtained EPR parameters to theoretical results. Based on the new assignment, trapping site, rotation, ortho-para conversion, quantum diffusion and isotope effect of H+ have been reinterpreted by the precise reanalysis as follows. The H6+ ion is composed of the collinearly aligned H2+ core at the center and two H2 rotors at both ends, occupies a single substitutional site, and has a precession motion around a crystalline axis with the angle of approximately 57 degrees. The ortho-para conversion of H2+ core of H6+ is completed within the time-scale of hours, whereas ortho-H2 molecules near H6+ convert much faster. H6+ diffuses quantum mechanically by the repetition of H6+ + H2 --> H2 + H6+ reaction. The diffusion terminates by the reaction, H6(+) + HD --> H5D(+) + H2, with a HD impurity contained in the para-H2 sample at natural abundance. Finally, we will propose a possible reason why H6+ is produced instead of H3+ in the irradiated solid H2.

Optical properties of InN thin films

NASA Astrophysics Data System (ADS)

Malakhov, Vladislav Y.

2000-04-01

The basic optical properties of low temperature plasma enhanced chemical reactionary sputtered (PECRS) InN thin films are presented. Optical absorption and reflectance spectra of InN polycrystalline films at room temperature in visible and near infrared (NIR) regions were taken to determine direct band gap energy (2.03 eV), electron plasma resonances energy (0.6 eV), damping constant (0.18 eV), and optical effective mass of electrons (0.11). In addition the UV and visible reflectance spectra have been used to reproduce accurately dielectric function of wurtzite InN for assignments of the peak structures to interband transitions (1.5 - 12.0 eV) as well as to determine dielectric constant (9.3) and refractive index (>3.0). The revealed reflectance peaks at 485 and 590 cm-1 respectively in IR spectra are connected with TO and LO optical vibration modes of InN films. Some TO (485 cm-1) and LO (585 cm-1) phonon features of indium nitride polycrystalline films on ceramics were observed in Raman spectra and also discussed. The excellent possibilities of InN polycrystalline layers for potential application in optoelectronic devices such as LEDs based InGaAlN and high efficiency solar cells are confirmed.

Syntheses and multi-NMR study of fac- and mer-OsO(3)F(2)(NCCH(3)) and the X-ray crystal structure (n = 2) and Raman spectrum (n = 0) of fac-OsO(3)F(2)(NCCH(3)).nCH(3)CN.

PubMed

Hughes, Michael J; Gerken, Michael; Mercier, Hélène P A; Schrobilgen, Gary J

2010-06-07

Dissolution of the infinite chain polymer, (OsO(3)F(2))(infinity), in CH(3)CN solvent at -40 degrees C followed by solvent removal under vacuum at -40 degrees C yielded fac-OsO(3)F(2)(NCCH(3)).nCH(3)CN (n >/= 2). Continued pumping at -40 degrees C with removal of uncoordinated CH(3)CN yielded fac-OsO(3)F(2)(NCCH(3)). Both fac-OsO(3)F(2)(NCCH(3)).nCH(3)CN and fac-OsO(3)F(2)(NCCH(3)) are yellow-brown solids and were characterized by low-temperature (-150 degrees C) Raman spectroscopy. The crystal structure (-173 degrees C) of fac-OsO(3)F(2)(NCCH(3)).2CH(3)CN consists of two co-crystallized CH(3)CN molecules and a pseudo-octahedral OsO(3)F(2).NCCH(3) molecule in which three oxygen atoms are in a facial arrangement and CH(3)CN is coordinated trans to an oxygen atom in an end-on fashion. The Os---N bond length (2.205(3) A) is among the shortest M---N adduct bonds observed for a d(0) transition metal oxide fluoride. The (19)F NMR spectrum of (OsO(3)F(2))(infinity) in CH(3)CN solvent (-40 degrees C) is a singlet (-99.6 ppm) corresponding to fac-OsO(3)F(2)(NCCH(3)). The (1)H, (15)N, (13)C, and (19)F NMR spectra of (15)N-enriched OsO(3)F(2)(NCCH(3)) were recorded in SO(2)ClF solvent (-84 degrees C). Nitrogen-15 enrichment resulted in splitting of the (19)F resonance of fac-OsO(3)F(2)((15)NCCH(3)) into a doublet ((2)J((15)N-(19)F), 21 Hz). In addition, a doublet of doublets ((2)J((19)F(ax)-(19)F(eq)), 134 Hz; (2)J((15)N-(19)F(eq)), 18 Hz) and a doublet ((2)J((19)F(ax)-(19)F(eq)), 134 Hz) were observed in the (19)F NMR spectrum that have been assigned to mer-OsO(3)F(2)((15)NCCH(3)); however, coupling of (15)N to the axial fluorine-on-osmium environment could not be resolved. The nitrogen atom of CH(3)CN is coordinated trans to a fluorine ligand in the mer-isomer. Quantum-chemical calculations at the SVWN and B3LYP levels of theory were used to calculate the energy-minimized gas-phase geometries, vibrational frequencies of fac- and mer-OsO(3)F(2)(NCCH(3)) and of CH(3)CN. The

Room temperature exciton-polariton resonant reflection and suppressed absorption in periodic systems of InGaN quantum wells

NASA Astrophysics Data System (ADS)

Bolshakov, A. S.; Chaldyshev, V. V.; Zavarin, E. E.; Sakharov, A. V.; Lundin, W. V.; Tsatsulnikov, A. F.; Yagovkina, M. A.

2017-04-01

We studied the optical properties of periodic InGaN/GaN multiple quantum well systems with different numbers of periods. A resonant increase in the optical reflection and simultaneous suppression of the optical absorption have been revealed experimentally at room temperature when the Bragg and exciton resonances were tuned to each other. Numerical modeling with a single set of parameters gave a quantitatively accurate fit of the experimental reflection and transmission spectra in a wide wavelength range and various angles of the light incidence. The model included both exciton resonance and non-resonant band-to-band transitions in the InGaN quantum wells, as well as Rayleigh light scattering in the GaN buffer layer. The analysis also involved x-ray diffraction and photoluminescence data. It allowed us to determine the key parameters of the structure. In particular, the radiative broadening of the InGaN QW excitons was evaluated as 0.20 ± 0.02 meV.

1.5-Tesla Multiparametric-Magnetic Resonance Imaging for the detection of clinically significant prostate cancer.

PubMed

Popita, Cristian; Popita, Anca Raluca; Sitar-Taut, Adela; Petrut, Bogdan; Fetica, Bogdan; Coman, Ioan

2017-01-01

Multiparametric-magnetic resonance imaging (mp-MRI) is the main imaging modality used for prostate cancer detection. The aim of this study is to evaluate the diagnostic performance of mp-MRI at 1.5-Tesla (1.5-T) for the detection of clinically significant prostate cancer. In this ethical board approved prospective study, 39 patients with suspected prostate cancer were included. Patients with a history of positive prostate biopsy and patients treated for prostate cancer were excluded. All patients were examined at 1.5-T MRI, before standard transrectal ultrasonography-guided biopsy. The overall sensitivity, specificity, positive predictive value and negative predictive value for mp-MRI were 100%, 73.68%, 80% and 100%, respectively. Our results showed that 1.5 T mp-MRI has a high sensitivity for detection of clinically significant prostate cancer and high negative predictive value in order to rule out significant disease.

Field-theoretical description of electromagnetic Δ resonance production and determination of the magnetic moment of the Δ+ (1232) resonance by the ep → e' N' π' γ' and γp → N' π' γ' reactions

NASA Astrophysics Data System (ADS)

Machavariani, A. I.; Faessler, Amand; Buchmann, A. J.

1999-02-01

The ep → e' N' π' γ' and γp → N' π' γ' reactions in the Δ resonance region are investigated in the framework of the relativistic field-theoretical spectral decomposition method for the γ ∗N → γ'π'N' transition amplitude. This approach allows us to express the amplitude through three-dimensional diagrams with on-mass shell intermediate states. The Δ resonance is constructed as intermediate cluster state | ΨΔ> with real bare mass MΔ ˜ 1232 MeV and with a complex propagator of Breit-Wigner shape for the P33 π N amplitude. Thus, the usual off-mass shell ambiguities in spin {3}/{2} effective Lagrangians do not affect the present description. Using a unified treatment of nucleons, mesons, and Δ's as bound systems of quarks according to the Haag-Nishijima-Zimmermann field-theoretical approach, it is shown that quark-gluon degrees of freedom only change the rule for constructing the form factors in three-dimensional diagrams for obtaining the γ ∗N → γ'π'N' transition amplitude. However, the structure of these-dimensional diagrams remains the same as in formulations with only meson and nucleon degrees of freedom. A simple redefinition of the γ ∗N → γ'π'N' amplitude which insures gauge invariance in every order of perturbation theory with an arbitrary choice of phenomenological vertices is considered. We calculate the leading diagram of this amplitude in the Δ resonance region. It is demonstrated that the differential cross section of the ep → e' N' π' γ' and γp → N' π' γ' reactions is sensitive to the value of the magnetic moment of the Δ+ resonance. Thus, the measurement of the differential cross section for ep → e' N' π' γ' and γp → N' π' γ' reactions can be used for determining the magnetic dipole moment of Δ+.

CARBON-RICH PRESOLAR GRAINS FROM MASSIVE STARS: SUBSOLAR {sup 12}C/{sup 13}C AND {sup 14}N/{sup 15}N RATIOS AND THE MYSTERY OF {sup 15}N

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pignatari, M.; Zinner, E.; Hoppe, P.

2015-08-01

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 (LD) 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 {sup 12}C/{sup 13}C and {sup 14}N/{sup 15}N 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 aremore » considered. If the supernova 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 {sup 13}C and {sup 15}N. The short-lived radionuclides {sup 22}Na and {sup 26}Al are increased by orders of magnitude. The production of radiogenic {sup 22}Ne from the decay of {sup 22}Na in the He shell might solve the puzzle of the Ne-E(L) component in LD graphite grains. This scenario is attractive for the SiC grains of type AB with {sup 14}N/{sup 15}N ratios lower than solar, and provides an alternative solution for SiC grains originally classified as nova grains. Finally, this process may contribute to the production of {sup 14}N and {sup 15}N in the Galaxy, helping to produce the {sup 14}N/{sup 15}N ratio in the solar system.« less

δ15N value does not reflect fasting in mysticetes.

PubMed

Aguilar, Alex; Giménez, Joan; Gómez-Campos, Encarna; Cardona, Luís; Borrell, Asunción

2014-01-01

The finding that tissue δ(15)N values increase with protein catabolism has led researchers to apply this value to gauge nutritive condition in vertebrates. However, its application to marine mammals has in most occasions failed. We investigated the relationship between δ(15)N values and the fattening/fasting cycle in a model species, the fin whale, a migratory capital breeder that experiences severe seasonal variation in body condition. We analyzed two tissues providing complementary insights: one with isotopic turnover (muscle) and one that keeps a permanent record of variations in isotopic values (baleen plates). In both tissues δ(15)N values increased with intensive feeding but decreased with fasting, thus contradicting the pattern previously anticipated. The apparent inconsistency during fasting is explained by the fact that a) individuals migrate between different isotopic isoscapes, b) starvation may not trigger significant negative nitrogen balance, and c) excretion drops and elimination of 15N-depleted urine is minimized. Conversely, when intensive feeding is resumed in the northern grounds, protein anabolism and excretion start again, triggering 15N enrichment. It can be concluded that in whales and other mammals that accrue massive depots of lipids as energetic reserves and which have limited access to drinking water, the δ15N value is not affected by fasting and therefore cannot be used as an indication of nutritive condition.

Hydrogen exchange kinetics in a membrane protein determined by sup 15 N NMR spectroscopy: Use of the INEPT (insensitive nucleus enhancement by polarization transfer) experiment to follow individual amides in detergent-solubilized M13 coat protein

DOE Office of Scientific and Technical Information (OSTI.GOV)

Henry, G.D.; Sykes, B.D.

The coat protein of the filamentous coliphage M13 is a 50-residue polypeptide which spans the inner membrane of the Escherichia coli host upon infection. Amide hydrogen exchange kinetics have been used to probe the structure and dynamics of M13 coat protein which has been solubilized in sodium dodecyl sulfate (SDS) micelles. In a previous {sup 1}H nuclear magnetic resonance (NMR) study, multiple exponential analysis of the unresolved amide proton envelope revealed the existence of two slow kinetic sets containing a total of about 30 protons. The slower set (15-20 amides) originates from the hydrophobic membrane-spanning region and exchanges at leastmore » 10{sup 5}-fold slower than the unstructured, non-H-bonded model polypeptide poly(DL-alanine). Herein the authors use {sup 15}N NMR spectroscopy of biosynthetically labeled coat protein to follow individual, assigned, slowly exchanging amides in or near the hydrophobic segment. The INEPT (insensitive nucleus enhancement by polarization transfer) experiments can be used to transfer magnetization to the {sup 15}N nucleus from a coupled proton; when {sup 15}N-labeled protonated protein is dissolved in {sup 2}H{sub 2}O, the INEPT signal disappears with time as the amide protons are replaced by solvent deuterons. Amide hydrogen exchange is catalyzed by both H{sup +} and OH{sup {minus}} ions. The time-dependent exchange-out experiment is suitable for slow exchange rates (k{sub ex}). The INEPT experiment was also adapted to measure some of the more rapidly exchanging amides in the coat protein using either saturation transfer from water or exchange effects on the polarization transfer step itself. The results of all of these experiments are consistent with previous models of the coat protein in which a stable segment extends from the hydrophobic membrane-spanning region through to the C-terminus, whereas the N-terminal region is undergoing more extensive dynamic fluctuations.« less

Selective Adsorption Resonances in the Scattering of n-H2 p-H2 n-D2 and o-D2 from Ag(111)

NASA Astrophysics Data System (ADS)

Yu, Chien-Fan; Whaley, K. Birgitta; Hogg, Charles S.; Sibener, Steven J.

1983-12-01

Diffractive and rotationally mediated selective adsorption scattering resonances are reported for n-H2 p-H2 n-D2 and o-D2 on Ag(111). Small resonance shifts and line-width differences are observed between n-H2 and p-H2 indicating a weak orientation dependence of the laterally averaged H2/Ag(111) potential. The p-H2 and o-D2 levels were used to determine the isotropic component of this potential, yielding a well depth of ~ 32 meV.

The "Speedy" Synthesis of Atom-Specific (15)N Imino/Amido-Labeled RNA.

PubMed

Neuner, Sandro; Santner, Tobias; Kreutz, Christoph; Micura, Ronald

2015-08-10

Although numerous reports on the synthesis of atom-specific (15)N-labeled nucleosides exist, fast and facile access to the corresponding phosphoramidites for RNA solid-phase synthesis is still lacking. This situation represents a severe bottleneck for NMR spectroscopic investigations on functional RNAs. Here, we present optimized procedures to speed up the synthesis of (15)N(1) adenosine and (15)N(1) guanosine amidites, which are the much needed counterparts of the more straightforward-to-achieve (15)N(3) uridine and (15)N(3) cytidine amidites in order to tap full potential of (1)H/(15)N/(15)N-COSY experiments for directly monitoring individual Watson-Crick base pairs in RNA. Demonstrated for two preQ1 riboswitch systems, we exemplify a versatile concept for individual base-pair labeling in the analysis of conformationally flexible RNAs when competing structures and conformational dynamics are encountered. © 2015 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim.

Defect states in hexagonal boron nitride: Assignments of observed properties and prediction of properties relevant to quantum computation

NASA Astrophysics Data System (ADS)

Sajid, A.; Reimers, Jeffrey R.; Ford, Michael J.

2018-02-01

Key properties of nine possible defect sites in hexagonal boron nitride (h-BN), VN,VN -1,CN,VNO2 B,VNNB,VNCB,VBCN,VBCNS iN , and VNCBS iB , are predicted using density-functional theory and are corrected by applying results from high-level ab initio calculations. Observed h-BN electron-paramagnetic resonance signals at 22.4, 20.83, and 352.70 MHz are assigned to VN,CN, and VNO2 B , respectively, while the observed photoemission at 1.95 eV is assigned to VNCB . Detailed consideration of the available excited states, allowed spin-orbit couplings, zero-field splitting, and optical transitions is made for the two related defects VNCB and VBCN . VNCB is proposed for realizing long-lived quantum memory in h-BN. VBCN is predicted to have a triplet ground state, implying that spin initialization by optical means is feasible and suitable optical excitations are identified, making this defect of interest for possible quantum-qubit operations.

Various vibration modes in a silicon ring resonator driven by p–n diode actuators formed in the lateral direction

NASA Astrophysics Data System (ADS)

Tsushima, Takafumi; Asahi, Yoichi; Tanigawa, Hiroshi; Furutsuka, Takashi; Suzuki, Kenichiro

2018-06-01

In this paper, we describe p–n diode actuators that are formed in the lateral direction on resonators. Because previously reported p–n diode actuators, which were driven by a force parallel to the electrostatic force induced in a p–n diode, were fabricated in the perpendicular direction to the surface, the fabrication process to satisfy the requirement of realizing a p–n junction set in the middle of the plate thickness has been difficult. The resonators in this work are driven by p–n diodes formed in the lateral direction, making the process easy. We have fabricated a silicon ring resonator that has in-plane vibration using p–n–p and n–p–n diode actuators formed in the lateral direction. First, we consider a space charge model that can sufficiently accurately describe the force induced in p–n diode actuators and compare it with the capacitance model used in most computer simulations. Then, we show that multiplying the vibration amplitude calculated by computer simulation by the modification coefficient of 4/3 provides the vibration amplitude in the p–n diode actuators. Good agreement of the theory with experimental results of the in-plane vibration measured for silicon ring resonators is obtained. The computer simulation is very useful for evaluating various vibration modes in resonators driven by the p–n diode actuators. The small amplitude of the p–n diode actuator measured in this work is expected to increase greatly with increased doping of the actuator.

Stable isotope tracking of endangered sea turtles: validation with satellite telemetry and δ15N analysis of amino acids.

PubMed

Seminoff, Jeffrey A; Benson, Scott R; Arthur, Karen E; Eguchi, Tomoharu; Dutton, Peter H; Tapilatu, Ricardo F; Popp, Brian N

2012-01-01

Effective conservation strategies for highly migratory species must incorporate information about long-distance movements and locations of high-use foraging areas. However, the inherent challenges of directly monitoring these factors call for creative research approaches and innovative application of existing tools. Highly migratory marine species, such as marine turtles, regularly travel hundreds or thousands of kilometers between breeding and feeding areas, but identification of migratory routes and habitat use patterns remains elusive. Here we use satellite telemetry in combination with compound-specific isotope analysis of amino acids to confirm that insights from bulk tissue stable isotope analysis can reveal divergent migratory strategies and within-population segregation of foraging groups of critically endangered leatherback sea turtles (Dermochelys coriacea) across the Pacific Ocean. Among the 78 turtles studied, we found a distinct dichotomy in δ(15)N values of bulk skin, with distinct "low δ(15)N" and "high δ(15)N" groups. δ(15)N analysis of amino acids confirmed that this disparity resulted from isotopic differences at the base of the food chain and not from differences in trophic position between the two groups. Satellite tracking of 13 individuals indicated that their bulk skin δ(15)N value was linked to the particular foraging region of each turtle. These findings confirm that prevailing marine isoscapes of foraging areas can be reflected in the isotopic compositions of marine turtle body tissues sampled at nesting beaches. We use a Bayesian mixture model to show that between 82 and 100% of the 78 skin-sampled turtles could be assigned with confidence to either the eastern Pacific or western Pacific, with 33 to 66% of all turtles foraging in the eastern Pacific. Our forensic approach validates the use of stable isotopes to depict leatherback turtle movements over broad spatial ranges and is timely for establishing wise conservation efforts in

As-Grown Gallium Nitride Nanowire Electromechanical Resonators

NASA Astrophysics Data System (ADS)

Montague, Joshua R.

Technological development in recent years has led to a ubiquity of micro- and nano-scale electromechanical devices. Sensors for monitoring temperature, pressure, mass, etc., are now found in nearly all electronic devices at both the industrial and consumer levels. As has been true for integrated circuit electronics, these electromechanical devices have continued to be scaled down in size. For many nanometer-scale structures with large surface-to-volume ratio, dissipation (energy loss) becomes prohibitively large causing a decreasing sensitivity with decreasing sensor size. In this work, gallium nitride (GaN) nanowires are investigated as singly-clamped (cantilever) mechanical resonators with typical mechanical quality factors, Q (equal to the ratio of resonance frequency to peak full-width-at-half-maximum-power) and resonance frequencies, respectively, at or above 30,000, and near 1 MHz. These Q values---in vacuum at room temperature---indicate very low levels of dissipation; they are essentially the same as those for bulk quartz crystal resonators that form the basis of simple clocks and mass sensors. The GaN nanowires have lengths and diameters, respectively, of approximately 15 micrometers and hundreds of nanometers. As-grown GaN nanowire Q values are larger than other similarly-sized, bottom-up, cantilever resonators and this property makes them very attractive for use as resonant sensors. We demonstrate the capability of detecting sub-monolayer levels of atomic layer deposited (ALD) films, and the robust nature of the GaN nanowires structure that allows for their 'reuse' after removal of such layers. In addition to electron microscope-based measurement techniques, we demonstrate the successful capacitive detection of a single nanowire using microwave homodyne reflectometry. This technique is then extended to allow for simultaneous measurements of large ensembles of GaN nanowires on a single sample, providing statistical information about the distribution of

1.5-Tesla Multiparametric-Magnetic Resonance Imaging for the detection of clinically significant prostate cancer

PubMed Central

POPITA, CRISTIAN; POPITA, ANCA RALUCA; SITAR-TAUT, ADELA; PETRUT, BOGDAN; FETICA, BOGDAN; COMAN, IOAN

2017-01-01

Background and aim Multiparametric-magnetic resonance imaging (mp-MRI) is the main imaging modality used for prostate cancer detection. The aim of this study is to evaluate the diagnostic performance of mp-MRI at 1.5-Tesla (1.5-T) for the detection of clinically significant prostate cancer. Methods In this ethical board approved prospective study, 39 patients with suspected prostate cancer were included. Patients with a history of positive prostate biopsy and patients treated for prostate cancer were excluded. All patients were examined at 1.5-T MRI, before standard transrectal ultrasonography–guided biopsy. Results The overall sensitivity, specificity, positive predictive value and negative predictive value for mp-MRI were 100%, 73.68%, 80% and 100%, respectively. Conclusion Our results showed that 1.5 T mp-MRI has a high sensitivity for detection of clinically significant prostate cancer and high negative predictive value in order to rule out significant disease. PMID:28246496

Vibrational spectrum of the K-590 intermediate in the bacteriorhodopsin photocycle at room temperature: picosecond time-resolved resonance coherent anti-Raman spectroscopy

NASA Astrophysics Data System (ADS)

Ujj, L.; Jäger, F.; Popp, A.; Atkinson, G. H.

1996-12-01

The vibrational spectrum of the K-590 intermediate, thought to contribute significantly to the energy storage and transduction mechanism in the bacteriorhodopsin (BR) photocycle, is measured at room temperature using picosecond time-resolved resonance coherent anti-Stokes Raman scattering (PTR/CARS). The room-temperature BR photocycle is initiated by the 3 ps, 570 nm excitation of the ground-state species, BR-570, prepared in both H 2O and D 2O suspensions of BR. PTR/CARS data, recorded 50 ps after BR-570 excitation, at which time only BR-570 and K-590 are present, have an excellent S/N which provides a significantly more detailed view of the K-590 vibrational degrees of freedom than previously available. Two picosecond (6 ps FWHM) laser pulses, ω1 (633.4 nm) and ωS (675-700 nm), are used to record PTR/CARS data via electronic resonance enhancement in both BR-570 and K-590, each of which contains a distinct retinal structure (assigned as 13- rans, 15- anti, 13- cis, respectively). To obtain the vibrational spectrum of K-590 separately, the PTR/CARS spectra from the mixture of isomeric retinals is quantitatively analyzed in terms of third-order susceptibility ( η(3)) relationships. PTR/CARS spectra of K-590 recorded from both H 2O and D 2O suspensions of BR are compared with the analogous vibrational data obtained via spontaneous resonance Raman (RR) scattering at both low (77 K) and room temperature. Analyses of these vibrational spectra identify temperature-dependent effects and changes assignable to the substitution of deuterium at the Schiff-base nitrogen not previously reported.

Rivermouth alteration of agricultural impacts on consumer tissue δ15N

USGS Publications Warehouse

Larson, James H.; Richardson, William B.; Vallazza, Jonathan M.; Nelson, J. C.

2013-01-01

Terrestrial agricultural activities strongly influence riverine nitrogen (N) dynamics, which is reflected in the δ15N of riverine consumer tissues. However, processes within aquatic ecosystems also influence consumer tissue δ15N. As aquatic processes become more important terrestrial inputs may become a weaker predictor of consumer tissue δ15N. In a previous study, this terrestrial-consumer tissue δ15N 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 δ15N 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.

The impact of electrode materials on 1/f noise in piezoelectric AlN contour mode resonators

NASA Astrophysics Data System (ADS)

Kim, Hoe Joon; Jung, Soon In; Segovia-Fernandez, Jeronimo; Piazza, Gianluca

2018-05-01

This paper presents a detailed analysis on the impact of electrode materials and dimensions on flicker frequency (1/f) noise in piezoelectric aluminum nitride (AlN) contour mode resonators (CMRs). Flicker frequency noise is a fundamental noise mechanism present in any vibrating mechanical structure, whose sources are not generally well understood. 1 GHz AlN CMRs with three different top electrode materials (Al, Au, and Pt) along with various electrode lengths and widths are fabricated to control the overall damping acting on the device. Specifically, the use of different electrode materials allows control of thermoelastic damping (TED), which is the dominant damping mechanism for high frequency AlN CMRs and largely depends on the thermal properties (i.e. thermal diffusivities and expansion coefficients) of the metal electrode rather than the piezoelectric film. We have measured Q and 1/f noise of 68 resonators and the results show that 1/f noise decreases with increasing Q, with a power law dependence that is about 1/Q4. Interestingly, the noise level also depends on the type of electrode materials. Devices with Pt top electrode demonstrate the best noise performance. Our results help unveiling some of the sources of 1/f noise in these resonators, and indicate that a careful selection of the electrode material and dimensions could reduce 1/f noise not only in AlN-CMRs, but also in various classes of resonators, and thus enable ultra-low noise mechanical resonators for sensing and radio frequency applications.

On the measurement of 15N-{1H} nuclear Overhauser effects. 2. Effects of the saturation scheme and water signal suppression

PubMed Central

Ferrage, Fabien; Reichel, Amy; Battacharya, Shibani; Cowburn, David; Ghose, Ranajeet

2013-01-01

Measurement of steady-state 15N-{1H} nuclear Overhauser effects forms a cornerstone of most methods to determine protein backbone dynamics from spin-relaxation data, since it is the most reliable probe of very fast motions on the ps-ns timescale. We have, in two previous publications (J. Magn. Reson. 192 (2008), 302-313; J. Am. Chem. Soc. 131 (2009), 6048-6049) reevaluated spin-dynamics during steady-state (or “saturated”) and reference experiments, both of which are required to determine the NOE ratio. Here we assess the performance of several windowed and windowless sequences to achieve effective saturation of protons in steady-state experiments. We also evaluate the influence of the residual water signal due to radiation damping on the NOE ratio. We suggest a recipe that allows one to determine steady-state 15N-{1H} NOE's without artifacts and with the highest possible accuracy. PMID:20951618

Interresidue carbonyl-carbonyl polarization transfer experiments in uniformly 13C, 15N-labeled peptides and proteins

NASA Astrophysics Data System (ADS)

Janik, Rafal; Ritz, Emily; Gravelle, Andrew; Shi, Lichi; Peng, Xiaohu; Ladizhansky, Vladimir

2010-03-01

In this work, we demonstrate that Homonuclear Rotary Resonance Recoupling (HORROR) can be used to reintroduce carbonyl-carbonyl interresidue dipolar interactions and to achieve efficient polarization transfer between carbonyl atoms in uniformly 13C, 15N-labeled peptides and proteins. We show that the HORROR condition is anisotropically broadened and overall shifted to higher radio frequency intensities because of the CSA effects. These effects are analyzed theoretically using Average Hamiltonian Theory. At spinning frequencies used in this study, 22 kHz, this broadening is experimentally found to be on the order of a kilohertz at a proton field of 600 MHz. To match HORROR condition over all powder orientations, variable amplitude radio frequency (RF) fields are required, and efficient direct transfers on the order of 20-30% can be straightforwardly established. Two- and three-dimensional chemical shift correlation experiments establishing long-range interresidue connectivities (e.g., (N[i]-CO[i - 2])) are demonstrated on the model peptide N-acetyl-valine-leucine, and on the third immunoglobulin binding domain of protein G. Possible future developments are discussed.

HNCA-TOCSY-CANH experiments with alternate 13C-12C labeling: a set of 3D experiment with unique supra-sequential information for mainchain resonance assignment

PubMed Central

Takeuchi, Koh; Gal, Maayan; Takahashi, Hideo; Shimada, Ichio

2011-01-01

Described here is a set of three-dimensional (3D) NMR experiments that rely on CACA-TOCSY magnetization transfer via the weak 3JCαCα coupling. These pulse sequences, which resemble recently described 13C detected CACA-TOCSY (Takeuchi et al. 2010) experiments, are recorded in 1H2O, and use 1H excitation and detection. These experiments require alternate 13C-12C labeling together with perdeuteration, which allows utilizing the small 3JCαCα scalar coupling that is otherwise masked by the stronger 1JCC couplings in uniformly 13C labeled samples. These new experiments provide a unique assignment ladder-mark that yields bidirectional supra-sequential information and can readily straddle proline residues. Unlike the conventional HNCA experiment, which contains only sequential information to the 13Cα of the preceding residue, the 3D hnCA-TOCSY-caNH experiment can yield sequential correlations to alpha carbons in positions i−1, i + 1 and i−2. Furthermore, the 3D hNca-TOCSY-caNH and Hnca-TOC-SY-caNH experiments, which share the same magnetization pathway but use a different chemical shift encoding, directly couple the 15N-1H spin pair of residue i to adjacent amide protons and nitrogens at positions i−2, i−1, i + 1 and i + 2, respectively. These new experimental features make protein backbone assignments more robust by reducing the degeneracy problem associated with the conventional 3D NMR experiments. PMID:21110064

Long-term 15N tracking from biological N fixation across different plant and humus components of the boreal forest

NASA Astrophysics Data System (ADS)

Arroniz-Crespo, Maria; Jones, David L.; Zackrisson, Olle; Nilsson, Marie-Charlotte; DeLuca, Thomas H.

2014-05-01

Biological N2 fixation by cyanobacteria associated with feather mosses is an important cog in the nitrogen (N) cycle of boreal forests; still, our understanding of the turnover and fate of N fixed by this association remains greatly incomplete. The 15N signature of plants and soil serves as a powerful tool to explore N dynamics in forest ecosystems. In particular, in the present study we aimed to investigate the contribution of N2 fixation to δ15N signatures of plants and humus component of the boreal forest. Here we present results from a long-term (7 years) tacking of labelled 15N2 across the humus layer, seedlings of the tree species Pinus sylvestris, two common dwarf shrub species (Empetrum hermaphroditum and Vaccinium vitis-idaea) and the feather moss Pleurozium schreibery. The enriched experiment was conducted in 2005 in a natural boreal forest in northern Sweden. Two different treatments (10% 15N2 headspace enrichment and control) were setup in nine different plots (0.5 x 0.5 m) within the forest. We observed a significant reduction of δ15N signature of the 15N-enriched moss that could be explained by a growth dilution effect. Nevertheless, after 5 years since 15N2 enrichment some of the label 15N was still detected on the moss and in particular in the dead tissue. We could not detect a clear transfer of the labelled 15N2 from the moss-cyanobacteria system to other components of the ecosystem. However, we found consistence relationship through time between increments of δ15N signature of some of the forest components in plots which exhibited higher N fixation rates in the moss. In particular, changes in natural abundance δ15N that could be associated with N fixation were more apparent in the humus layer, the dwarf shrub Vaccinium vitis-idaea and the pine seedlings when comparing across plots and years.

Removal of slow-pulsing artifacts in in-phase 15N relaxation dispersion experiments using broadband 1H decoupling.

PubMed

Chatterjee, Soumya Deep; Ubbink, Marcellus; van Ingen, Hugo

2018-06-02

Understanding of the molecular mechanisms of protein function requires detailed insight into the conformational landscape accessible to the protein. Conformational changes can be crucial for biological processes, such as ligand binding, protein folding, and catalysis. NMR spectroscopy is exquisitely sensitive to such dynamic changes in protein conformations. In particular, Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments are a powerful tool to investigate protein dynamics on a millisecond time scale. CPMG experiments that probe the chemical shift modulation of 15 N in-phase magnetization are particularly attractive, due to their high sensitivity. These experiments require high power 1 H decoupling during the CPMG period to keep the 15 N magnetization in-phase. Recently, an improved version of the in-phase 15 N-CPMG experiment was introduced, offering greater ease of use by employing a single 1 H decoupling power for all CPMG pulsing rates. In these experiments however, incomplete decoupling of off-resonance amide 1 H spins introduces an artefactual dispersion of relaxation rates, the so-called slow-pulsing artifact. Here, we analyze the slow-pulsing artifact in detail and demonstrate that it can be suppressed through the use of composite pulse decoupling (CPD). We report the performances of various CPD schemes and show that CPD decoupling based on the 90 x -240 y -90 x element results in high-quality dispersion curves free of artifacts, even for amides with high 1 H offset.

GaN microring waveguide resonators bonded to silicon substrate by a two-step polymer process.

PubMed

Hashida, Ryohei; Sasaki, Takashi; Hane, Kazuhiro

2018-03-20

Using a polymer bonding technique, GaN microring waveguide resonators were fabricated on a Si substrate for future hybrid integration of GaN and Si photonic devices. The designed GaN microring consisted of a rib waveguide having a core of 510 nm in thickness, 1000 nm in width, and a clad of 240 nm in thickness. A GaN crystalline layer of 1000 nm in thickness was grown on a Si(111) substrate by metal organic chemical vapor deposition using a buffer layer of 300 nm in thickness for the compensation of lattice constant mismatch between GaN and Si crystals. The GaN/Si wafer was bonded to a Si(100) wafer by a two-step polymer process to prevent it from trapping air bubbles. The bonded GaN layer was thinned from the backside by a fast atom beam etching to remove the buffer layer and to generate the rib waveguides. The transmission characteristics of the GaN microring waveguide resonators were measured. The losses of the straight waveguides were measured to be 4.0±1.7  dB/mm around a wavelength of 1.55 μm. The microring radii ranged from 30 to 60 μm, where the measured free-spectral ranges varied from 2.58 to 5.30 nm. The quality factors of the microring waveguide resonators were from 1710 to 2820.

δ(15) N from soil to wine in bulk samples and proline.

PubMed

Paolini, Mauro; Ziller, Luca; Bertoldi, Daniela; Bontempo, Luana; Larcher, Roberto; Nicolini, Giorgio; Camin, Federica

2016-09-01

The feasibility of using δ(15) N as an additional isotopic marker able to link wine to its area of origin was investigated. The whole production chain (soil-leaves-grape-wine) was considered. Moreover, the research included evaluation of the effect of the fermentation process, the use of different types of yeast and white and red vinification, the addition of nitrogen adjuvants and ultrasound lysis simulating wine ageing. The δ(15) N of grapes and wine was measured in bulk samples and compounds, specifically in proline, for the first time. Despite isotopic fractionation from soil to wine, the δ(15) N values of leaves, grapes, wine and particularly must and wine proline conserved the variability of δ(15) N in the growing soil. Fermentation and ultrasound treatment did not affect the δ(15) N values of grape must, which was therefore conserved in wine. The addition of inorganic or organic adjuvants was able to influence the δ(15) N of bulk wine, depending on the amount and the difference between the δ(15) N of must and that of the adjuvant. The δ(15) N of wine proline was not influenced by adjuvant addition and is therefore the best marker for tracing the geographical origin of wine. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Human dietary δ(15)N intake: representative data for principle food items.

PubMed

Huelsemann, F; Koehler, K; Braun, H; Schaenzer, W; Flenker, U

2013-09-01

Dietary analysis using δ(15)N values of human remains such as bone and hair is usually based on general principles and limited data sets. Even for modern humans, the direct ascertainment of dietary δ(15)N is difficult and laborious, due to the complexity of metabolism and nitrogen fractionation, differing dietary habits and variation of δ(15)N values of food items. The objective of this study was to summarize contemporary regional experimental and global literature data to ascertain mean representative δ(15)N values for distinct food categories. A comprehensive data set of more than 12,000 analyzed food samples was summarized from the literature. Data originated from studies dealing with (1) authenticity tracing or origin control of food items, and (2) effects of fertilization or nutrition on δ(15)N values of plants or animals. Regional German food δ(15)N values revealed no major differences compared with the mean global values derived from the literature. We found that, in contrast to other food categories, historical faunal remains of pig and poultry are significantly enriched in (15)N compared to modern samples. This difference may be due to modern industrialized breeding practices. In some food categories variations in agricultural and feeding regimens cause significant differences in δ(15)N values that may lead to misinterpretations when only limited information is available. Copyright © 2013 Wiley Periodicals, Inc.

Simultaneous acquisition of 2D and 3D solid-state NMR experiments for sequential assignment of oriented membrane protein samples.

PubMed

Gopinath, T; Mote, Kaustubh R; Veglia, Gianluigi

2015-05-01

We present a new method called DAISY (Dual Acquisition orIented ssNMR spectroScopY) for the simultaneous acquisition of 2D and 3D oriented solid-state NMR experiments for membrane proteins reconstituted in mechanically or magnetically aligned lipid bilayers. DAISY utilizes dual acquisition of sine and cosine dipolar or chemical shift coherences and long living (15)N longitudinal polarization to obtain two multi-dimensional spectra, simultaneously. In these new experiments, the first acquisition gives the polarization inversion spin exchange at the magic angle (PISEMA) or heteronuclear correlation (HETCOR) spectra, the second acquisition gives PISEMA-mixing or HETCOR-mixing spectra, where the mixing element enables inter-residue correlations through (15)N-(15)N homonuclear polarization transfer. The analysis of the two 2D spectra (first and second acquisitions) enables one to distinguish (15)N-(15)N inter-residue correlations for sequential assignment of membrane proteins. DAISY can be implemented in 3D experiments that include the polarization inversion spin exchange at magic angle via I spin coherence (PISEMAI) sequence, as we show for the simultaneous acquisition of 3D PISEMAI-HETCOR and 3D PISEMAI-HETCOR-mixing experiments.

Extrinsic Tryptophans as NMR Probes of Allosteric Coupling in Membrane Proteins: Application to the A2A Adenosine Receptor.

PubMed

Eddy, Matthew T; Gao, Zhan-Guo; Mannes, Philip; Patel, Nilkanth; Jacobson, Kenneth A; Katritch, Vsevolod; Stevens, Raymond C; Wüthrich, Kurt

2018-06-20

Tryptophan indole 15 N- 1 H signals are well separated in nuclear magnetic resonance (NMR) spectra of proteins. Assignment of the indole 15 N- 1 H signals therefore enables one to obtain site-specific information on complex proteins in supramacromolecular systems, even when extensive assignment of backbone 15 N- 1 H resonances is challenging. Here we exploit the unique indole 15 N- 1 H chemical shift by introducing extrinsic tryptophan reporter residues at judiciously chosen locations in a membrane protein for increased coverage of structure and function by NMR. We demonstrate this approach with three variants of the human A 2A adenosine receptor (A 2A AR), a class A G protein-coupled receptor, each containing a single extrinsic tryptophan near the receptor intracellular surface, in helix V, VI, or VII, respectively. We show that the native A 2A AR global protein fold and ligand binding activity are preserved in these A 2A AR variants. The indole 15 N- 1 H signals from the extrinsic tryptophan reporter residues show different responses to variable efficacy of drugs bound to the receptor orthosteric cavity, and the indole 15 N- 1 H chemical shift of the tryptophan introduced at the intracellular end of helix VI is sensitive to conformational changes resulting from interactions with a polypeptide from the carboxy terminus of the Gα S intracellular partner protein. Introducing extrinsic tryptophans into proteins in complex supramolecular systems thus opens new avenues for NMR investigations in solution.

15N-metabolic labeling for comparative plasma membrane proteomics in Arabidopsis cells.

PubMed

Lanquar, Viviane; Kuhn, Lauriane; Lelièvre, Françoise; Khafif, Mehdi; Espagne, Christelle; Bruley, Christophe; Barbier-Brygoo, Hélène; Garin, Jérôme; Thomine, Sébastien

2007-03-01

An important goal for proteomic studies is the global comparison of proteomes from different genotypes, tissues, or physiological conditions. This has so far been mostly achieved by densitometric comparison of spot intensities after protein separation by 2-DE. However, the physicochemical properties of membrane proteins preclude the use of 2-DE. Here, we describe the use of in vivo labeling by the stable isotope 15N as an alternative approach for comparative membrane proteomic studies in plant cells. We confirm that 15N-metabolic labeling of proteins is possible and efficient in Arabidopsis suspension cells. Quantification of 14N versus 15N MS signals reflects the relative abundance of 14N and 15N proteins in the sample analyzed. We describe the use of 15N-metabolic labeling to perform a partial comparative analysis of Arabidopsis cells following cadmium exposure. By focusing our attention on plasma membrane proteins, we were able to confidently identify proteins showing up to 5-fold regulation compared to unexposed cells. This study provides a proof of principle that 15N-metabolic labeling is a useful technique for comparative membrane proteome studies.