<Superscript>1</Superscript>H, <Superscript>13</Superscript>C,and <Superscript>15</Superscript>N resonance assignments for the pro-inflammatory cytokine interleukin-36α

Interleukin-36α (IL-36α) is a recently characterised member of the interleukin-1 superfamily. It is involved in the pathogenesis of inflammatory arthritis in one third of psoriasis patients. By binding of IL-36α to its receptor IL-36R via the NF-κB pathway other cytokines involved in inflammatory and apoptotic cascade are activated. The efficacy of complex formation is controlled by N-terminal processing. To obtain a more detailed view on the structure function relationship we performed a heteronuclear multidimensional NMR investigation and here report the ¹H, ¹³C, and ¹⁵N resonance assignments for the backbone and side chain nuclei of the pro-inflammatory cytokine interleukin-36α.     

Sequence specific <Superscript>1</Superscript>H, <Superscript>13</Superscript>C and <Superscript>15</Superscript>N resonance assignments of a cataract-related variant G57W of human γS-crystallin

γS-crystallin is a major structural component of the human eye lens, which maintains its stability over the lifetime of an organism with negligible turnover. The G57W mutant of human γS-crystallin (abbreviated hereafter as γS-G57W) is associated with dominant congenital cataracts. In order to provide a structural basis for the ability of γS-G57W causing cataract, we have cloned, overexpressed, isolated and purified the protein. The 2D [¹⁵N–¹H]-HSQC spectrum recorded with uniformly ¹³C/¹⁵N-labelled γS-G57W was highly dispersed indicating the protein to adopt an ordered conformation. In this paper, we report almost complete sequence-specific ¹H, ¹³C and ¹⁵N resonance assignments of γS-G57W using a suite of heteronuclear 3D NMR experiments.     

Coral skeletal carbon isotopes (δ<Superscript>13</Superscript>C and Δ<Superscript>14</Superscript>C) record the delivery of terrestrial carbon to the coastal waters of Puerto Rico

Tropical small mountainous rivers deliver a poorly quantified, but potentially significant, amount of carbon to the world’s oceans. However, few historical records of land–ocean carbon transfer exist for any region on Earth. Corals have the potential to provide such records, because they draw on dissolved inorganic carbon (DIC) for calcification. In temperate systems, the stable- (δ¹³C) and radiocarbon (Δ¹⁴C) isotopes of coastal DIC are influenced by the δ¹³C and Δ¹⁴C of the DIC transported from adjacent rivers. A similar pattern should exist in tropical coastal DIC and hence coral skeletons. Here, δ¹³C and Δ¹⁴C measurements were made in a 56-year-old Montastraea faveolata coral growing ~1 km from the mouth of the Rio Fajardo in eastern Puerto Rico. Additionally, the δ¹³C and Δ¹⁴C values of the DIC of the Rio Fajardo and its adjacent coastal waters were measured during two wet and dry seasons. Three major findings were observed: (1) synchronous depletions of both δ¹³C and Δ¹⁴C in the coral skeleton are annually coherent with the timing of peak river discharge, (2) riverine DIC was always more depleted in δ¹³C and Δ¹⁴C than seawater DIC, and (3) the correlation of δ¹³C and Δ¹⁴C was the same in both coral skeleton and the DIC of the river and coastal waters. These results indicate that coral skeletal δ¹³C and Δ¹⁴C are recording the delivery of riverine DIC to the coastal ocean. Thus, coral records could be used to develop proxies of historical land–ocean carbon flux for many tropical regions. Such information could be invaluable for understanding the role of tropical land–ocean carbon flux in the context of land-use change and global climate change.     

The trophic history of Myall Lakes,New South Wales,Australia: interpretations using δ<Superscript>13</Superscript>C and δ<Superscript>15</Superscript>N of the sedimentary record

In an attempt to determine the trophic history of the Myall Lakes complex (New South Wales, Australia) δ¹³C_org, δ¹⁵N and C_org:N profiles were determined for bulk organic matter of two short sediment cores from Bombah Broadwater and Myall Lake. ²¹⁰Pb profiles and sediment types indicate significantly different trophic trajectories during the time periods examined. δ¹³C_org and C_org:N indicate Bombah Broadwater has been dominated by increasing inputs of terrestrial organic material over the last century, thought to be related to watershed disturbance including agricultural activity. Primary production appears to be dominated by phytoplankton. δ¹⁵N remained relatively stable at around 1‰ until the mid–1970s when there was a sharp increase to 4.7‰, interpreted as an influx of sewage-derived material. These observations offer an insight into the recent trophic changes at the site. Sedimentation rates are noticeably lower in Myall Lake and the most recent sediment is a flocculent organic rich deposit overlying mineral clay. δ¹³C_org and C_org:N values indicate a transition from plankton to macrophyte dominated primary production around 1800AD. δ¹⁵N values become increasingly negative from approximately 1900AD. This is interpreted as being due to increasing reliance by macrophytes on nitrogen recycled from decomposing sediments driven by natural infilling and eutrophication in this basin. The contrasting sedimentation rates, sediment types and geochemical profiles suggest the different basins of this water body are subject to substantially different internal and external influences which should be considered in management decisions.     

Synthesis of the β-amyloid fragment <Superscript>5</Superscript>RHDSGY<Superscript>10</Superscript> and its isomers

The peptide RHDSGY, a fragment of the human β-amyloid Zn-binding site, and its isomers RH(D-Asp)SGY and RH(β-Asp)SGY have been obtained as amides by means of solid-phase synthesis and analyzed by HPLC and various mass spectrometric methods. The problem of low yield of the RHDSGY peptide and its isomers attributed to 9-fluorenylmethoxycarbonyl (Fmoc)-amino acids and/or formation of such side-products as RH(β-Asp)SGY (or RHDSGY during synthesis of RH(β-Asp)SGY) and RH(Asp-imide) SGY was solved via selection of individual reagents for removal of Fmoc groups from α-amino groups of the growing peptide chain.     

Accurate measurement of <Superscript>15</Superscript>N–<Superscript>13</Superscript>C residual dipolar couplings in nucleic acids

New 3D HCN quantitative J (QJ) pulse schemes are presented for the precise and accurate measurement of one-bond ¹⁵N_1/9–¹³C₁, ¹⁵N_1/9–¹³C_6/8, and ¹⁵N_1/9–¹³C_2/4 residual dipolar couplings (RDCs) in weakly aligned nucleic acids. The methods employ ¹H–¹³C multiple quantum (MQ) coherence or TROSY-type pulse sequences for optimal resolution and sensitivity. RDCs are obtained from the intensity ratio of H₁–C₁–N_1/9 (MQ-HCN-QJ) or H_6/8–C_6/8–N_1/9 (TROSY-HCN-QJ) correlations in two interleaved 3D NMR spectra, with dephasing intervals of zero (reference spectrum) and 1/(2J_NC) (attenuated spectrum). The different types of ¹⁵N–¹³C couplings can be obtained by using either the 3D MQ-HCN-QJ or TROSY-HCN-QJ pulse scheme, with the appropriate setting of the duration of the constant-time ¹⁵N evolution period and the offset of two frequency-selective ¹³C pulses. The methods are demonstrated for a uniformly ¹³C, ¹⁵N-enriched 24-nucleotide stem-loop RNA sequence, helix-35, aligned in the magnetic field using phage Pf1. For measurements of RDCs systematic errors are found to be negligible, and experiments performed on a 1.5 mM helix-35 sample result in an estimated precision of ca. 0.07 Hz for ¹D_NC, indicating the utility of the measured RDCs in structure validation and refinement. Indeed, for a complete set of ¹⁵N_1/9–¹³C₁, ¹⁵N_1/9–¹³C_6/8, and ¹⁵N_1/9–¹³C_2/4 dipolar couplings obtained for the stem nucleotides, the measured RDCs are in excellent agreement with those predicted for an NMR structure of helix-35, refined using independently measured observables, including ¹³C–¹H, ¹³C–¹³C and ¹H–¹H dipolar couplings.Supplementary material to this paper is available in electronic form at http://dx.doi.org/10.1007/s10858-005-0646-2.     

CACA-TOCSY with alternate <Superscript>13</Superscript>C–<Superscript>12</Superscript>C labeling: a <Superscript>13</Superscript>C<Superscript>α</Superscript> direct detection experiment for mainchain resonance assignment,dihedral angle information,and amino acid type identification

We present a ¹³C direct detection CACA-TOCSY experiment for samples with alternate ¹³C–¹²C labeling. It provides inter-residue correlations between ¹³C^α resonances of residue i and adjacent C^αs at positions i − 1 and i + 1. Furthermore, longer mixing times yield correlations to C^α nuclei separated by more than one residue. The experiment also provides C^α-to-sidechain correlations, some amino acid type identifications and estimates for ψ dihedral angles. The power of the experiment derives from the alternate ¹³C–¹²C labeling with [1,3-¹³C] glycerol or [2-¹³C] glycerol, which allows utilizing the small scalar ³J_CC couplings that are masked by strong ¹J_CC couplings in uniformly ¹³C labeled samples.     

Determination of the lifetime of D<Stack><Subscript>2</Subscript><Superscript>−</Superscript></Stack> and HD<Superscript>−</Superscript> ions

A method for determining the lifetime of unstable ions is described. The method is based on measuring the decrease in the ion beam current onto a fixed detector with increasing path length of the ion beam from the ion source to the detector. The measurements performed for D^? ₂ and HD^? molecular ions have shown that their lifetimes are 3.5 ± 0.1 and 4.4 ± 0.1 μs, respectively.     

Foliar δ<Superscript>13</Superscript>C values of nine dominant species in the Loess Plateau of China

The foliar stable carbon isotope compositions (δ¹³C) of nine dominant species in seven sites, Yangling, Yongshou, Tongchuan, Fuxian, Ansai, Mizhi, and Shenmu, standing from the south to the north in the Loess Plateau of China were studied. The results showed that foliar δ¹³C values ranged from −22.61 to −30.73 ‰ with an average of −27.23 ‰ in 141 C₃ plant samples collected from the Loess Plateau. Foliar δ¹³C values varied significantly (p<0.001) among the nine C₃ species, which were Pinus tabulaeformis Carr., Robinia pseudoacacia L., Zizyphus jujuba Mill. var. spinosus Hu., Rubus parvifolius L., Hippophae rhamnoides L., Caragana korshinskii Kom., Lespedeza davurica (Laxm.) Schindl., Artemisia sacrorum Ledeb. var. incana Mattf., and Agropyron cristatum Gaertn. Comparatively, R. pseudoacacia, H. rhamnoides, and C. korshinskii had much higher δ¹³C values than the other six species, while A. sacrorum had the lowest δ¹³C value. There was no significant difference in foliar δ¹³C value among five species, P. tabulaeformis, Z. jujuba, R. parvifolius, L. davurica, and A. cristatum. Considering the life forms categorized from nine C₃ species, trees and shrubs had significantly higher δ¹³C values than herbs (p<0.001). The deciduous tree R. pseudoacacia had much higher δ¹³C value than the evergreen tree P. tabulaeformis (p<0.01). Among the four shrubs, foliar δ¹³C values in H. rhamnoides and C. korshinskii were markedly higher (p<0.01) than those in Z. jujuba and R. parvifolius. Among the three herbs, L. davurica and A. cristatum had significantly higher δ¹³C values than A. sacrorum (p<0.01). Leguminous species such as R. pseudoacacia, C. korshinskii, and L. davurica as well as a non-leguminous species with nitrogen-fixation capacity, H. rhamnoides, had higher δ¹³C values than other non-leguminous species with same life-form. The mean δ¹³C value increased by about 7 % from Yangling in the south to Shenmu in the north as climatic drought increased, and foliar δ¹³C values differed much (p<0.001) among the seven sites. For nine species in the Loess Plateau, foliar δ¹³C values were significantly and negatively (p<0.001) correlated with the mean annual precipitation, moreover, an increase of 100 mm in annual precipitation would result in a decrease of 1.2 ‰ in δ¹³C value.     

Estimation of denitrification potential in a karst aquifer using the <Superscript>15</Superscript>N and <Superscript>18</Superscript>O isotopes of NO<Stack><Subscript>3</Subscript><Superscript>−</Superscript></Stack>

A confined aquifer in the Malm Karst of the Franconian Alb, South Germany was investigated in order to understand the role of the vadose zone in denitrifiaction processes. The concentrations of chemical tracers Sr²⁺ and Cl^– and concentrations of stable isotope ¹⁸O were measured in spring water and precipitation during storm events. Based on these measurements a conceptual model for runoff was constructed. The results indicate that pre-event water, already stored in the system at the beginning of the event, flows downslope on vertical and lateral preferential flow paths. Chemical tracers used in a mixing model for hydrograph separation have shown that the pre-event water contribution is up to 30%. Applying this information to a conceptual runoff generation model, the values of ¹⁵N and ¹⁸O in nitrate could be calculated. Field observations showed the occurence of significant microbial denitrification processes above the soil/bedrock interface before nitrate percolates through to the deeper horizon of the vadose zone. The source of nitrate could be determined and denitrification processes were calculated. Assuming that the nitrate reduction follows a Rayleigh process one could approximate a nitrate input concentration of about 170 mg/l and a residual nitrate concentration of only about 15%. The results of the chemical and isotopic tracers postulate fertilizers as nitrate source with some influence of atmospheric nitrate. The combined application of hydrograph separation and determination of isotope values in ¹⁵N and ¹⁸O of nitrate lead to an improved understanding of microbial processes (nitrification, denitrification) in dynamic systems.     

Selective suppression of excipient signals in 2D <Superscript>1</Superscript>H–<Superscript>13</Superscript>C methyl spectra of biopharmaceutical products

While the use of ¹H–¹³C methyl correlated NMR spectroscopy at natural isotopic abundance has been demonstrated as feasible on protein therapeutics as large as monoclonal antibodies, spectral interference from aliphatic excipients remains a significant obstacle to its widespread application. These signals can cause large baseline artifacts, obscure protein resonances, and cause dynamic range suppression of weak peaks in non-uniform sampling applications, thus hampering both traditional peak-based spectral analyses as well as emerging chemometric methods of analysis. Here we detail modifications to the 2D ¹H–¹³C gradient-selected HSQC experiment that make use of selective pulsing techniques for targeted removal of interfering excipient signals in spectra of the NISTmAb prepared in several different formulations. This approach is demonstrated to selectively reduce interfering excipient signals while still yielding 2D spectra with only modest losses in protein signal. Furthermore, it is shown that spectral modeling based on the SMILE algorithm can be used to simulate and subtract any residual excipient signals and their attendant artifacts from the resulting 2D NMR spectra.     

Sensitive <Superscript>13</Superscript>C–<Superscript>13</Superscript>C correlation spectra of amyloid fibrils at very high spinning frequencies and magnetic fields

Sensitive 2D solid-state ¹³C–¹³C correlation spectra of amyloid β fibrils have been recorded at very fast spinning frequencies and very high magnetic fields. It is demonstrated that PARIS-xy recoupling using moderate rf amplitudes can provide structural information by promoting efficient magnetization transfer even under such challenging experimental conditions. Furthermore, it has been shown both experimentally and by numerical simulations that the method is not very sensitive to dipolar truncation effects and can reveal direct transfer across distances of about 3.5–4Å.     

Tracking the fate of digesta <Superscript>13</Superscript>C and <Superscript>15</Superscript>N compositions along the ruminant gastrointestinal tract: Does digestion influence the relationship between diet and faeces?

Faecal stable isotope compositions reflect wildlife diets, if digestive processes along the gastrointestinal tract (GIT) do not alter diet–faeces isotopic relationships in an unpredictable way. We investigated ¹³C and ¹⁵N compositions of digesta along the ruminant GIT, using Saanen dairy goats kept on pure grass hay or browse for >20 days. Isotopic changes occurred in the ventral rumen, and in the small intestine, where digesta had significantly higher δ¹³C and δ¹⁵N (associated with lower C or higher N content, respectively) values relative to other GIT sites. However, effects on isotope fractionation were small (∼1.0‰ for δ¹³C and ∼ 2.0‰ for δ¹⁵N), and were reversed in the hindgut such that faecal isotope compositions did not differ from the foregut. No other substantial isotopic changes occurred across GIT sites, despite the morphophysiological complexity of the ruminant GIT. We found similarly small differences across GIT components of rheem gazelles (Gazella leptoceros) fed a mixture of C₃ lucerne and C₄ grass, although in this case faeces were ¹⁵N-depleted relative to other GIT components. Along with differences in δ¹⁵N between goats fed browse or grass, this result implies a systematic difference in diet–faeces δ¹⁵N relationships, contingent on the botanical composition of ruminant diets. Thus, while our results support faecal δ¹³C as a reliable proxy for wildlife diets, further work on factors influencing faecal ¹⁵N abundance is needed. Finally, we note high levels of isotopic variability between individuals fed the same diets, even accounting for the relatively short duration of the experiments, suggesting an important influence of stochasticity on isotope fractionation.