Effects of N-application on utilization of 15N and 13C and quality in two wheat cultivars

We studied N uptake and distribution in wheat, and the incorporation of nitrogen and carbon into gluten and non-gluten proteins using a double-labelling approach with ¹⁵N and ¹³C. Doses of N-fertilizer were split and applied at emergence, onset of stem elongation, and heading at rates of 280/140/140 mg N pot^?1, respectively simulating 90/45/45 kg N ha^?1. Five different combinations of N-fertilizations containing no or 10 % ¹⁵N were performed. The recovery of ¹⁵N added at the stages emergence, stem elongation or heading were 42, 60, and 64 %. Application of ¹⁵N at all three stages yielded in 51 % recovery. Remobilisation of straw N was greater for Golia. The ¹⁵N concentration in gluten proteins of Golia show higher values than Gönen. The ratio of ¹⁵N gluten/¹⁵N non-gluten proteins of Golia were higher, which implies a lower non-gluten protein activity during grain filling. The ¹³C concentration in gluten and non-gluten proteins did not differ between both cultivars.     

15N allocation into wheat grains (Triticum aestivum L.) influenced by sowing rate and water supply at flowering under a Mediterranean climate

This study examined the effects of a reduced wheat sowing rate (250 vs. 500 grains m^–2) on grain yield, uptake of ¹⁵N into grains, and the incorporation into gluten and non-gluten proteins of wheat under field conditions in the Aegean region. A single ¹⁵N application was applied at stem elongation, at flowering, or at both developmental stages. Each ¹⁵N treatment included either additional water supply, or no additional water supply at flowering. Sowing rate (either 250 or 500 grains m^–2) had no impact on grain yield. Grain yield increased with additional water supply, but at the expense of protein quality, because of a decrease in the protein content of gluten. The ¹⁵N content of the gluten and non-gluten proteins at grain maturity was not different among cultivars. ¹⁵N applied at both stem elongation and flowering was found in comparable amounts in grains and protein fractions, irrespective of sowing rate.     

Feeding level and diet quality influence trophic shift of C and N isotopes in Nile tilapia (Oreochromis niloticus (L.))

Many scientists use naturally occurring stable isotopes to reconstruct the diets of animals. However, isotopic ratios may be affected not only by the composition of the diet but also by the amount of food consumed. Thus, an experiment using tilapia (Oreochromis niloticus) was carried out to test the influence of feeding level on delta13C and delta15N of fish given a semi-synthetic wheat gluten/wheat starch based diet. In addition, the effect of diet quality was tested by comparing tilapia given this feed with tilapia fed a fish meal/wheat meal based diet. Forty-four tilapia were reared individually. After a prefeeding phase, fish were randomly assigned to five groups, four on the semi-synthetic diet at different feeding levels and one group on the fish meal/wheat meal based diet fed at the equivalent of the highest level of the semi-synthetic diet. The experiment lasted eight weeks. Proximate composition, gross energy content and delta13C and delta15N values were determined in feed and fish, for delta13C separately in the lipids and the lipid-free matter. Delta13C in the lipids and the lipid-free matter and delta15N of tilapia fed the semi-synthetic diet decreased significantly with increasing feeding rate. The absolute values of the trophic shift in fish fed the semi-synthetic wheat based diet were significantly higher than in fish fed the fish meal/wheat meal based diet. The different delta13C and delta15N values in tilapia fed the same diet at different feeding levels and the influence of feed quality on the trophic shift add to the uncertainty involved in the use of stable isotopes in ecological research.     

Triple resonance experiments for aligned sample solid-state NMR of (13)C and (15)N labeled proteins

Initial steps in the development of a suite of triple-resonance (1)H/(13)C/(15)N solid-state NMR experiments applicable to aligned samples of (13)C and (15)N labeled proteins are described. The experiments take advantage of the opportunities for (13)C detection without the need for homonuclear (13)C/(13)C decoupling presented by samples with two different patterns of isotopic labeling. In one type of sample, the proteins are approximately 20% randomly labeled with (13)C in all backbone and side chain carbon sites and approximately 100% uniformly (15)N labeled in all nitrogen sites; in the second type of sample, the peptides and proteins are (13)C labeled at only the alpha-carbon and (15)N labeled at the amide nitrogen of a few residues. The requirement for homonuclear (13)C/(13)C decoupling while detecting (13)C signals is avoided in the first case because of the low probability of any two (13)C nuclei being bonded to each other; in the second case, the labeled (13)C(alpha) sites are separated by at least three bonds in the polypeptide chain. The experiments enable the measurement of the (13)C chemical shift and (1)H-(13)C and (15)N-(13)C heteronuclear dipolar coupling frequencies associated with the (13)C(alpha) and (13)C' backbone sites, which provide orientation constraints complementary to those derived from the (15)N labeled amide backbone sites. (13)C/(13)C spin-exchange experiments identify proximate carbon sites. The ability to measure (13)C-(15)N dipolar coupling frequencies and correlate (13)C and (15)N resonances provides a mechanism for making backbone resonance assignments. Three-dimensional combinations of these experiments ensure that the resolution, assignment, and measurement of orientationally dependent frequencies can be extended to larger proteins. Moreover, measurements of the (13)C chemical shift and (1)H-(13)C heteronuclear dipolar coupling frequencies for nearly all side chain sites enable the complete three-dimensional structures of proteins to be determined with this approach.     

Acquisition and loss of cryotolerance in Livistona chinensis embryos during seed development

Changes in desiccation tolerance and cryotolerance of chinese fan palm (Livistona chinensis [Jacq.] R. Br.) Embryos were studied during seed development from 15 to 45 weeks after flowering (WAF). Acquisition and then progressive loss in both desiccation tolerance and cryotolerance was observed within this period. Survival (apparent elongation of embryos) and emergence (formation of root and/or shoot) of embryos following dehydration increased progressively with development of seeds until 33 WAF, and then decreased up to 45 WAF. Similar changes occurred in the minimum moisture content at which 90% of embryos survived or emerged. Cryotolerance of embryos was nil at the early stages of seed development, until 21 WAF. Embryos acquired slight cryotolerance at 23 WAF and cryotolerance increased gradually from 27 to 36 WAF, then decreased by 45 WAF. Survival and emergence of post-thaw embryos were closely related to their moisture contents prior to freezing. However, this correlation between cryopreservation and moisture content was notably influenced by the embryos' developmental stage. Embryos at stages with greater cryotolerance gave higher post-thaw survival and emergence at a given moisture content, and the moisture content range allowing embryos to avoid cryo-damage was widened at both the lower and upper limits. Greater than 50% post-thaw emergence was observed only in embryos with moisture contents below 20% (fresh weight) at developmental stages between 27 and 36 WAF, although more than 90% of embryos could be dehydrated to < 20% moisture contents without loss in survival and emergence as early as 21WAF. Nearly 80% embryos could be dehydrated safely to 20% moisture content as late as 45 WAF.     

Distribution and utilization of 15N in cowpeas injected into the stem under influence of water deficit

Investigations were carried out on Vigna unguiculata L. Walp. to estimate the distribution and utilization of 15N in different organs after stem injection during vegetative, flowering and pod filling stage. During flowering effects of water deficit were also examined. In well watered plants, within 4 days after injection, 65% of 15N accumulated in leaves. This was drastically reduced to 42% by water deficit. 15N accumulation in stems increased under water deficit. The translocation of 15N from the stem base to roots were not altered by water deficit. During pod filling 62% of recovered 15N in the plants had accumulated in seeds, 24% in leaves and 11% in stems within 4 days, whereas the uptake of nitrogen in pod walls and roots remained low (2%). These results demonstrate that the method of injecting very small quantities (1 mg/plant) of 15N into the stem base allows an exact and detailed quantitative assessment of N translocation/distribution with regard to different organs, different growth stages and different treatments.     

Three-dimensional 13C shift/1H-15N coupling/15N shift solid-state NMR correlation spectroscopy.

Triple-resonance experiments capable of correlating directly bonded and proximate carbon and nitrogen backbone sites of uniformly 13C- and 15N-labeled peptides in stationary oriented samples are described. The pulse sequences integrate cross-polarization from 1H to 13C and from 13C to 15N with flip-flop (phase and frequency switched) Lee-Goldburg irradiation for both 13C homonuclear decoupling and 1H-15N spin exchange at the magic angle. Because heteronuclear decoupling is applied throughout, the three-dimensional pulse sequence yields 13C shift/1H-15N coupling/15N shift correlation spectra with single-line resonances in all three frequency dimensions. Not only do the three-dimensional spectra correlate 13C and 15N resonances, they are well resolved due to the three independent frequency dimensions, and they can provide up to four orientationally dependent frequencies as input for structure determination. These experiments have the potential to make sequential backbone resonance assignments in uniformly 13C- and 15N-labeled proteins.     

Stable carbon and nitrogen isotope signatures of root-holoparasitic Cynomorium songaricum and its hosts at the Tibetan plateau and the surrounding Gobi desert in China

We first measured the δ(13)C and δ(15)N values of root holoparasite Cynomorium songaricum and its hosts from 19 sites across four provinces in northwest China, in an attempt to investigate their nutritional relationship at the Tibetan plateau and the surrounding Gobi desert. Our study showed that the δ(13)C of C. songaricum closely mirrored the values of its hosts, Nitraria tangutorum and N. sibirica across all sampling sites. C. songaricum was significantly depleted in (13)C compared to host plants at the Tibetan plateau, showing an average parasite/host δ(13)C difference of-0.6?‰. In contrast, (15)N of C. songaricum was significantly enriched by+1.3?‰ compared to the hosts, implying that these holoparasites had other nitrogen resources. Although no difference in the δ(13)C and δ(15)N values between holoparasites and hosts was detected, the δ(13)C and δ(15)N values of holoparasites were significantly correlated with those of their hosts at the Gobi desert. The δ(13)C versus δ(15)N values were significantly but negatively correlated for the hosts; however, holoparasite/host variation in δ(13)C was not correlated with the variation in δ(15)N. The δ(13)C versus δ(15)N values were negatively correlated in C. songaricum, and this relationship tended to be magnified along the increasing elevations independent of the host plants. C. songaricum at the Tibetan plateau exhibited different δ(13)C and δ(15)N signatures compared with those at the Gobi desert. Furthermore, both δ(13)C and δ(15)N values of C. songaricum and its host plants in salt marshes at the Tibetan plateau were different from those in sand sites at the Tibetan plateau and the Gobi desert. Our results indicate that the isotopic difference depends on the different altitudes and habitats and is host-specific.     

Feeding level and diet quality influence trophic shift of c and n isotopes in nile tilapia (oreochromis niloticus (L.))

Many scientists use naturally occurring stable isotopes to reconstruct the diets of animals. However, isotopic ratios may be affected not only by the composition of the diet but also by the amount of food consumed. Thus, an experiment using tilapia (Oreochromis niloticus) was carried out to test the influence of feeding level on δ ¹³C and δ ¹⁵N of fish given a semi-synthetic wheat gluten/wheat starch based diet. In addition, the effect of diet quality was tested by comparing tilapia given this feed with tilapia fed a fish meal/wheat meal based diet. Forty-four tilapia were reared individually. After a prefeeding phase, fish were randomly assigned to five groups, four on the semi-synthetic diet at different feeding levels and one group on the fish meal/wheat meal based diet fed at the equivalent of the highest level of the semi-synthetic diet. The experiment lasted eight weeks. Proximate composition, gross energy content and δ ¹³C and δ ¹⁵N values were determined in feed and fish, for δ ¹³C separately in the lipids and the lipid-free matter. δ ¹³C in the lipids and the lipid-free matter and δ ¹⁵N of tilapia fed the semi-synthetic diet decreased significantly with increasing feeding rate. The absolute values of the trophic shift in fish fed the semi-synthetic wheat based diet were significantly higher than in fish fed the fish meal/wheat meal based diet. The different δ ¹³C and δ ¹⁵N values in tilapia fed the same diet at different feeding levels and the influence of feed quality on the trophic shift add to the uncertainty involved in the use of stable isotopes in ecological research.     

Correlation of backbone amide and side-chain (13)C resonances in perdeuterated proteins

Side-chain carbon resonance assignments are difficult to obtain for larger proteins. While standard methods require protons for excitation and detection of magnetization, their presence is often unacceptable and often leads to unacceptable relaxation losses at the directly bound carbon sites. In this paper, pulse sequences are presented which provide connectivities between aliphatic side-chain (13)C and amide (1)H and (15)N chemical shifts in fully deuterated, (13)C/(15)N-enriched proteins. Magnetization either starts off from carbons or from both nitrogens and protons and is passed along the side-chain via (13)C-(13)C isotropic mixing. Direct rather than (13)CO-relayed (15)N-->(13)C(alpha) or (13)C(alpha)-->(15)N transfer steps allow the detection of intraresidual as well as sequential correlations. To avoid ambiguities between these two types in the three-dimensional version of the experiments, a fourth dimension can be introduced to achieve their separation along a (13)C(alpha) frequency axis. The novel methods are demonstrated with the uniformly (2)H/(13)C/(15)N labeled 35-kDa protein diisopropylfluorophosphatase from Loligo vulgaris.     

Distribution and Utilization of 15N in Cowpeas Injected into the Stem Under Influence of Water Deficit

Abstract

Investigations were carried out on Vigna unguiculata L. Walp. to estimate the distribution and utilization of ¹⁵N in different organs after stem injection during vegetative, flowering and pod filling stage. During flowering effects of water deficit were also examined. In well watered plants, within 4 days after injection, 65% of ¹⁵N accumulated in leaves. This was drastically reduced to 42% by water deficit. ¹⁵N accumulation in stems increased under water deficit. The translocation of ¹⁵N from the stem base to roots were not altered by water deficit. During pod filling 62% of recovered ¹⁵N in the plants had accumulated in seeds, 24% in leaves and 11% in stems within 4 days, whereas the uptake of nitrogen in pod walls and roots remained low (2%). These results demonstrate that the method of injecting very small quantities (1 mg/plant) of ¹⁵N into the stem base allows an exact and detailed quantitative assessment of N translocation/distribution with regard to different organs, different growth stages and different treatments.     

Effect of partial recovery of zinc surface at room temperature after basal plane indentation

The effect of partial recovery of zinc surface at room temperature after basal plane indentation was detected and studied with a scanning tunneling microscope. It was found that indentation depth recovery depending on time occurs in one stage and recovery of lateral sizes in two stages with different activation energies, which are less than that of bulk zinc self-diffusion. Possible mechanisms of surface self-diffusion of zinc atoms leading to surface crystal growth were discussed. It was shown that the dynamics of effects observed on the sample surface in the indentation area after 15-min annealing at 100°C is associated with emergence of thermally generated vacancies from the sample bulk.     

Optimal control based NCO and NCA experiments for spectral assignment in biological solid-state NMR spectroscopy

We present novel pulse sequences for magic-angle-spinning solid-state NMR structural studies of (13)C,(15)N-isotope labeled proteins. The pulse sequences have been designed numerically using optimal control procedures and demonstrate superior performance relative to previous methods with respect to sensitivity, robustness to instrumental errors, and band-selective excitation profiles for typical biological solid-state NMR applications. Our study addresses specifically (15)N to (13)C coherence transfers being important elements in spectral assignment protocols for solid-state NMR structural characterization of uniformly (13)C,(15)N-labeled proteins. The pulse sequences are analyzed in detail and their robustness towards spin system and external experimental parameters are illustrated numerically for typical (15)N-(13)C spin systems under high-field solid-state NMR conditions. Experimentally the methods are demonstrated by 1D (15)N-->(13)C coherence transfer experiments, as well as 2D and 3D (15)N,(13)C and (15)N,(13)C,(13)C chemical shift correlation experiments on uniformly (13)C,(15)N-labeled ubiquitin.     

Alanine check points in HNN and HN(C)N spectra

Rapid resonance assignment is a key requirement in structural genomics research by NMR. In this context we present here two new pulse sequences, namely, HNN-A and HN(C)N-A that have been developed by simple modification of the previously described pulse sequences, HNN and HN(C)N [S.C. Panchal, N.S. Bhavesh, R.V. Hosur, Improved 3D triple resonance experiments, HNN and HN(C)N, for H(N) and 15N sequential correlations in (13C, 15N) labeled proteins: application to unfolded proteins, J. Biomol. NMR, 20 (2001) 135-147]. These increase the number of start/check points in HNN and/or HN(C)N spectra and hence help in pacing up resonance assignment in proteins.     

Frequency-selective heteronuclear dephasing and selective carbonyl labeling to deconvolute crowded spectra of membrane proteins by magic angle spinning NMR

We present a new method that combines carbonyl-selective labeling with frequency-selective heteronuclear recoupling to resolve the spectral overlap of magic angle spinning (MAS) NMR spectra of membrane proteins in fluid lipid membranes with broad lines and high redundancy in the primary sequence. We implemented this approach in both heteronuclear (15)N-(13)C(α) and homonuclear (13)C-(13)C dipolar assisted rotational resonance (DARR) correlation experiments. We demonstrate its efficacy for the membrane protein phospholamban reconstituted in fluid PC/PE/PA lipid bilayers. The main advantage of this method is to discriminate overlapped (13)C(α) resonances by strategically labeling the preceding residue. This method is highly complementary to (13)C(i-1)(')-(15)N(i)-(13)C(i)(α) and (13)C(i-1)(α)-(15)N(i-1)-(13)C(i)(') experiments to distinguish inter-residue spin systems at a minimal cost to signal-to-noise.     

A 'just-in-time' HN(CA)CO experiment for the backbone assignment of large proteins with high sensitivity

Among the suite of commonly used backbone experiments, HNCACO presents an unresolved sensitivity limitation due to fast 13CO transverse relaxation and passive 13Calpha-13Cbeta coupling. Here, we present a high-sensitivity 'just-in-time' (JIT) HN(CA)CO pulse sequence that uniformly refocuses 13Calpha-13Cbeta coupling while collecting 13CO shifts in real time. Sensitivity comparisons of the 3-D JIT HN(CA)CO, a CT-HMQC-based control, and a HSQC-based control with selective 13Calpha inversion pulses were performed using a 2H/13C/15N labeled sample of the 29 kDa HCA II protein at 15 degrees C. The JIT experiment shows a 42% signal enhancement over the CT-HMQC-based experiment. Compared to the HSQC-based experiment, the JIT experiment is 16% less sensitive for residues experiencing proper 13Calpha refocusing and13Calpha-13Cbeta decoupling. However, for the remaining residues, the JIT spectrum shows a 106% average sensitivity gain over the HSQC-based experiment. The high-sensitivity JIT HNCACO experiment should be particularly beneficial for studies of large proteins to provide 13CO resonance information regardless of residue type.     

Side-chain H and C resonance assignment in protonated/partially deuterated proteins using an improved 3D(13)C-detected HCC-TOCSY

We propose the use of (13)C-detected 3D HCC-TOCSY experiments for assignment of (1)H and (13)C resonances in protonated and partially deuterated proteins. The experiments extend 2D C-13-start and C-13-observe TOCSY type experiments proposed earlier. Introduction of the third (1)H dimension to 2D TOCSY: (i) reduces the peak overlap and (ii) increases the sensitivity per unit time, even for highly deuterated (>85%) protein samples, which makes this improved method an attractive tool for the side-chain H and C assignment of average sized proteins with natural isotope abundance as well as large partially deuterated proteins. The experiments are demonstrated with a 16 kDa (15)N, (13)C-labeled non-deuterated apo-CcmE and a 48 kDa uniformly (15)N, (13)C-labeled and fractionally ( approximately 90%) deuterated dimeric sFkpA. It is predicted that this method should be suitable for the assignment of methyl (13)C and (1)H chemical shifts of methyl protonated, highly deuterated and (13)C-labeled proteins with even higher molecular weight.     

Sample optimization and identification of signal patterns of amino acid side chains in 2D RFDR spectra of the alpha-spectrin SH3 domain

Future structural investigations of proteins by solid-state CPMAS NMR will rely on uniformly labeled protein samples showing spectra with an excellent resolution. NMR samples of the solid alpha-spectrin SH3 domain were generated in four different ways, and their (13)C CPMAS spectra were compared. The spectrum of a [u-(13)C, (15)N]-labeled sample generated by precipitation shows very narrow (13)C signals and resolved scalar carbon-carbon couplings. Linewidths of 16-19 Hz were found for the three alanine C(beta )signals of a selectively labeled [70% 3-(13)C]alanine-enriched SH3 sample. The signal pattern of the isoleucine, of all prolines, valines, alanines, and serines, and of three of the four threonines were identified in 2D (13)C-(13)C RFDR spectra of the [u-(13)C, (15)N]-labeled SH3 sample. A comparison of the (13)C chemical shifts of the found signal patterns with the (13)C assignment obtained in solution shows an intriguing match.     

SPINAL modulated decoupling in high field double- and triple-resonance solid-state NMR experiments on stationary samples

Continuous wave irradiation has limited bandwidth for heteronuclear 1H decoupling at high fields and for 13C decoupling in 1H/13C/15N triple-resonance experiments. SPINAL-16 modulation is shown to improve the efficiency of 1H and 13C heteronuclear decoupling on single crystals of peptides and on magnetically aligned samples of membrane proteins in bicelles, which is of particular importance because aqueous samples of biomolecules are lossy at high fields, which limits the strengths of the RF fields that can be applied.     

A dual 13C and 15N long-term labelling technique to investigate uptake and translocation of C and N in beech (Fagus sylvatica L.)

A continuous dual 13CO2 and 15NH4(15)NO3 labelling experimental set-up is presented that was used to investigate the C and N uptake and allocation within 3-year old beech (Fagus sylvatica L.) during one growing season. The C and N allocation pattern was determined after six, twelve and eighteen weeks of growth. The carbon uptake was distinctly different in the three phases examined: The first six weeks after budbreak were dedicated to leaf growth with a R/S (root to shoot) ratio of 0.14 for the new carbon. The second growth phase showed a balanced R/S ratio of C allocation and after week 13, the root compartment was the main carbon sink (R/S = 6.97). Nitrogen allocation was more basipetal as compared to carbon. In the second growth phase, R/S of Nnew was 5.57 but fell to 3.54 for the third growth phase probably due to formation of reserves in buds and stem.