Computational and Empirical Trans-hydrogen Bond Deuterium Isotope Shifts Suggest that N1–N3 A:U Hydrogen Bonds of RNA are Shorter than those of A:T Hydrogen Bonds of DNA

Density functional theory calculations of isolated Watson–Crick A:U and A:T base pairs predict that adenine ¹³C2 trans-hydrogen bond deuterium isotope shifts due to isotopic substitution at the pyrimidine H3, ^2hΔ¹³C2, are sensitive to the hydrogen-bond distance between the N1 of adenine and the N3 of uracil or thymine, which supports the notion that ^2hΔ¹³C2 is sensitive to hydrogen-bond strength. Calculated ^2hΔ¹³C2 values at a given N1–N3 distance are the same for isolated A:U and A:T base pairs. Replacing uridine residues in RNA with 5-methyl uridine and substituting deoxythymidines in DNA with deoxyuridines do not statistically shift empirical ^2hΔ¹³C2 values. Thus, we show experimentally and computationally that the C7 methyl group of thymine has no measurable affect on ^2hΔ¹³C2 values. Furthermore, ^2hΔ¹³C2 values of modified and unmodified RNA are more negative than those of modified and unmodified DNA, which supports our hypothesis that RNA hydrogen bonds are stronger than those of DNA. It is also shown here that ^2hΔ¹³C2 is context dependent and that this dependence is similar for RNA and DNA. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Estimates of methyl 13C and 1H CSA values (Δσ) in proteins from cross-correlated spin relaxation

Simple pulse schemes are presented for the measurement of methyl ¹³C and ¹H CSA values from ¹H–¹³C dipole/¹³C CSA and ¹H–¹³C dipole/¹H CSA cross-correlated relaxation. The methodology is applied to protein L and malate synthase G. Average ¹³C CSA values are considerably smaller for Ile than Leu/Val (17 vs 25 ppm) and are in good agreement with previous solid state NMR studies of powders of amino acids and dipeptides and in reasonable agreement with quantum-chemical DFT calculations of methyl carbon CSA values in peptide fragments. Small averaged ¹H CSA values on the order of 1 ppm are measured, consistent with a solid state NMR determination of the methyl group ¹H CSA in dimethylmalonic acid.     

Dead wood biomass and turnover time,measured by radiocarbon,along a subalpine elevation gradient

Dead wood biomass can be a substantial fraction of stored carbon in forest ecosystems, and coarse woody debris (CWD) decay rates may be sensitive to climate warming. We used an elevation gradient in Colorado Rocky Mountain subalpine forest to examine climate and species effects on dead wood biomass, and on CWD decay rate. Using a new radiocarbon approach, we determined that the turnover time of lodgepole pine CWD (340±130 years) was roughly half as long in a site with 2.5–3°C warmer air temperature, as that of pine (630±400 years) or Engelmann spruce CWD (800±960 and 650±410 years) in cooler sites. Across all sites and both species, CWD age ranged from 2 to 600 years, and turnover time was 580±180 years. Total standing and fallen dead wood biomass ranged from 4.7±0.2 to 54±1 Mg ha^–1, and from 2.8 to 60% of aboveground live tree biomass. Dead wood biomass increased 75 kg ha^–1 per meter gain in elevation and decreased 13 Mg ha^–1 for every degree C increase in mean air temperature. Differences in biomass and decay rates along the elevation gradient suggest that climate warming will lead to a loss of dead wood carbon from subalpine forest.Electronic Supplementary Material Supplementary material is available for this article at     

NMR crystallography: The effect of deuteration on high resolution C solid state NMR spectra of a 7-TM protein

The effect of deuteration on the ¹³C linewidths of U-¹³C, ¹⁵N 2D crystalline bacteriorhodopsin (bR) from Halobacterium salinarium, a 248-amino acid protein with seven-transmembrane (7TM) spanning regions, has been studied in purple membranes as a prelude to potential structural studies. Spectral doubling of resonances was observed for receptor expressed in ²H medium (for both 50:50% 1H:2H, and a more highly deuterated form) with the resonances being of similar intensities and separated by < 0.3 ppm in the methyl spectral regions in which they were readily distinguished. Line-widths of the methyl side chains were not significantly altered when the protein was expressed in highly deuterated medium compared to growth in fully protonated medium (spectral line widths were about 0.5 ppm on average for receptor expressed both in the fully protonated and highly deuterated media from the Cδ, Cγ₁, and Cγ₂ Ile ¹³C signals observed in the direct, 21-39 ppm, and indirect, 9-17 ppm, dimensions). The measured ¹³C NMR line-widths observed for both protonated and deuterated form of the receptor are sufficiently narrow, indicating that this crystalline protein morphology is suitable for structural studies. ¹H decoupling comparison of the protonated and deuterated bR imply that deuteration may be advantageous for samples in which low power ¹H decoupling is required.     

Quantitative estimation of magnitude and orientation of the CSA tensor from field dependence of longitudinal NMR relaxation rates

A method is presented that makes it possible to estimate both the orientation and the magnitude of the chemical shift anisotropy (CSA) tensor in molecules with a pair of spin 1/2 nuclei, typically ¹³C-¹H or ¹⁵ N-¹H. The method relies on the fact that the longitudinal cross-correlation rate as well as a linear combination of the autorelaxation rates of longitudinal heterospin magnetization, longitudinal two-spin order and longitudinal proton magnetization are proportional to the spectral density at the Larmor frequency of the heterospin. Therefore the ratio between the cross-correlation rate and the above linear combination is independent of the dynamics. From the field dependence of the ratio both the magnitude and the orientation of the CSA tensor can be estimated. The method is applicable to molecules in all motional regimes and is not limited to molecules in extreme narrowing or slow tumbling, nor is it sensitive to chemical exchange broadening. It is tested on the 22 amino acid residue peptide motilin, selectively ¹³ C labeled in the ortho positions in the ring of the single tyrosine residue. In the approximation of an axially symmetric ¹³C CSA tensor, the symmetry axis of the CSA tensor makes an angle of 23° ± 1° to the ¹³ C-¹H bond vector, and has a magnitude of 156 ± 5 ppm. This is in close agreement with solid-state NMR data on tyrosine powder [Frydman et al. (1992) Isr. J. Chem., 32, 161–164].     

Isotopic enrichment in herbivorous insects: a comparative field-based study of variation

Researchers will be able to use stable isotope analysis to study community structure in an efficient way, without a need for extensive calibrations, if isotopic enrichment values are consistent, or if variation in enrichment values can be predicted. In this study, we generated an experimental data set of δ¹⁵N and δ¹³C enrichment means for 22 terrestrial herbivorous arthropods feeding on 18 different host plants. Mean enrichments observed across a single trophic transfer (plants to herbivores) were −0.53±0.26‰ for δ¹³C (range: −3.47‰ to 1.89‰) and 1.88±0.37‰ for δ¹⁵N (range: −0.20‰ to 6.59‰). The mean δ¹³C enrichment was significantly lower than that reported in recent literature surveys, whereas the mean δ¹⁵N enrichment was not significantly different. The experimental data set provided no support for recent hypotheses advanced to explain variation in enrichment values, including the proposed roles for consumer feeding mode, development type, and diet C:N ratio. A larger data set, formed by combining our experimental data with data from the literature, did suggest possible roles for feeding mode, nitrogen recycling, herbivore life stage, and host plant type. Our results indicate that species enrichment values are variable even in this relatively narrow defined group of organisms and that our ability to predict enrichment values of terrestrial herbivorous arthropods based on physiological, ecological, or taxonomic traits is low. The primary implications are that (1) mean enrichment may have to be measured empirically for each trophic link of interest, rather than relying on estimates from a broad survey of animal taxa and (2) the advantage of using stable isotope analysis to probe animal communities that are recalcitrant to other modes of study will be somewhat diminished as a consequence.Electronic Supplementary Material Supplementary material is available for this article at     

Synthetic analogues of the histidine–chlorophyll complex: a NMR study to mimic structural features of the photosynthetic reaction center and the light-harvesting complex

Mg(II)–porphyrin–ligand and (bacterio)chlorophyl–ligand coordination interactions have been studied by solution and solid-state MAS NMR spectroscopy. ¹H, ¹³C and ¹⁵N coordination shifts due to ring currents, electronic perturbations and structural effects are resolved for imidazole (Im) and 1-methylimidazole (1-MeIm) coordinated axially to Mg(II)-OEP and (B)Chl a. As a consequence of a single axial coordination of Im or 1-MeIm to the Mg(II) ion, 0.9–5.2 ppm ¹H, 0.2–5.5 ppm ¹³C and 2.1–27.2 ppm ¹⁵N coordination shifts were measured for selectively labeled [1,3-¹⁵N]-Im, [1,3-¹⁵N,2-¹³C]-Im and [1,3-¹⁵N,1,2-¹³C]-1-MeIm. The coordination shifts depend on the distance of the nuclei to the porphyrin plane and the perturbation of the electronic structure. The signal intensities in the ¹H NMR spectrum reveal a five-coordinated complex, and the isotropic chemical shift analysis shows a close analogy with the electronic structure of the BChl a–histidine in natural light harvesting 2 complexes. The line broadening of the ligand responses support the complementary IR data and provide evidence for a dynamic coordination bond in the complex.Abbreviations (B)Chl a (bacterio)chlorophyll a - HMBC heteronuclear multiple bond correlation - Im imidazole - LH light-harvesting - 1-MeIm 1-methylimidazole - Mg(II)-Por Mg(II)-porphyrin macrocycle - OEP 2,3,7,8,12,13,17,18-octaethylporphyrin     

Woody debris contribution to the carbon budget of selectively logged and maturing mid-latitude forests

Woody debris (WD) is an important component of forest C budgets, both as a C reservoir and source of CO₂ to the atmosphere. We used an infrared gas analyzer and closed dynamic chamber to measure CO₂ efflux from downed coarse WD (CWD; diameter≥7.5 cm) and fine WD (FWD; 7.5 cm>diameter≥2 cm) to assess respiration in a selectively logged forest and a maturing forest (control site) in the northeastern USA. We developed two linear regression models to predict WD respiration: one based on WD temperature, moisture, and size (R ²=0.57), and the other on decay class and air temperature (R ²=0.32). WD respiration (0.28±0.09 Mg C ha⁻¹ year⁻¹) contributed only ≈2% of total ecosystem respiration (12.3±0.7 Mg C ha⁻¹ year⁻¹, 1999–2003), but net C flux from CWD accounted for up to 30% of net ecosystem exchange in the maturing forest. C flux from CWD on the logged site increased modestly, from 0.61±0.29 Mg C ha⁻¹ year⁻¹ prior to logging to 0.77±0.23 Mg C ha⁻¹ year⁻¹ after logging, reflecting increased CWD stocks. FWD biomass and associated respiration flux were ≈7 times and ≈5 times greater, respectively, in the logged site than the control site. The net C flux associated with CWD, including inputs and respiratory outputs, was 0.35±0.19 Mg C ha⁻¹ year⁻¹ (net C sink) in the control site and −0.30±0.30 Mg C ha⁻¹ year⁻¹ (net C source) in the logged site. We infer that accumulation of WD may represent a small net C sink in maturing northern hardwood forests. Disturbance, such as selective logging, can enlarge the WD pool, increasing the net C flux from the WD pool to the atmosphere and potentially causing it to become a net C source.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Resolution-optimized NMR measurement of <Superscript>1</Superscript>D<Subscript>CH</Subscript>, <Superscript>1</Superscript>D<Subscript>CC</Subscript> and <Superscript>2</Superscript>D<Subscript>CH</Subscript> residual dipolar couplings in nucleic acid bases

New methods are described for accurate measurement of multiple residual dipolar couplings in nucleic acid bases. The methods use TROSY-type pulse sequences for optimizing resolution and sensitivity, and rely on the E.COSY principle to measure the relatively small two-bond ²D_CH couplings at high precision. Measurements are demonstrated for a 24-nt stem-loop RNA sequence, uniformly enriched in ¹³C, and aligned in Pf1. The recently described pseudo-3D method is used to provide homonuclear ¹H-¹H decoupling, which minimizes cross-correlation effects and optimizes resolution. Up to seven ¹H-¹³C and ¹³C-¹³C couplings are measured for pyrimidines (U and C), including ¹D_C5H5, ¹D_C6H6, ²D_C5H6, ²D_C6H5, ¹D_C5C4, ¹D_C5C6, and ²D_C4H5. For adenine, four base couplings (¹D_C2H2, ¹D_C8H8, ¹D_C4C5, and ¹D_C5C6) are readily measured whereas for guanine only three couplings are accessible at high relative accuracy (¹D_C8H8, ¹D_C4C5, and ¹D_C5C6). Only three dipolar couplings are linearly independent in planar structures such as nucleic acid bases, permitting cross validation of the data and evaluation of their accuracies. For the vast majority of dipolar couplings, the error is found to be less than ±3% of their possible range, indicating that the measurement accuracy is not limiting when using these couplings as restraints in structure calculations. Reported isotropic values of the one- and two-bond J couplings cluster very tightly for each type of nucleotide.     

Critical test of some computational methods for prediction of NMR <Superscript>1</Superscript>H and <Superscript>13</Superscript>C chemical shifts

Performance of 18 DFT functionals (B1B95, B3LYP, B3PW91, B97D, BHandHLYP, BMK, CAM-B3LYP, HSEh1PBE, M06-L, mPW1PW91, O3LYP, OLYP, OPBE, PBE1PBE, tHCTHhyb, TPSSh, wB97xD, VSXC) in combinations with six basis sets (cc-pVDZ, aug-cc-pVDZ, cc-pVTZ, aug-cc-pVTZ, IGLO-II, and IGLO-III) and three methods for calculating magnetic shieldings (GIAO, CSGT, IGAIM) was tested for predicting ¹H and ¹³C chemical shifts for 25 organic compounds, for altogether 86 H and 88 C atoms. Proton shifts varied between 1.03 ppm to 12.00 ppm and carbon shifts between 7.87 ppm to 209.28 ppm. It was found that the best method for calculating ¹³C shifts is PBE1PBE/aug-cc-pVDZ with CSGT or IGAIM approaches (mae?=?1.66 ppm), for ¹H the best results were obtained with HSEh1PBE, mPW1PW91, PBE1PBE, CAM-B3LYP, and B3PW91 functionals with cc-pVTZ basis set and with CSGT or IGAIM approaches (mae?=?0.28 ppm). We found that often larger basis sets do not give better results for chemical shifts. The best basis sets for calculating ¹H and ¹³C chemical shifts were cc-pVTZ and aug-cc-pVDZ, respectively. CSGT and IGAIM NMR approaches can perform really well and are in most cases better than popular GIAO approach.

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Graphical Abstract Mean absolute errors for ¹H and ¹³C chemical shifts and computational times of neutral toluene molecule with aug-cc-pVDZ basis set and CSGT approach

     

Characterization of polyhydroxyalkanoates accumulated by a moderately halophilic salt pan isolate Bacillus megaterium strain H16

Aim

Characterization of polyhydroxyalkanoates (PHA) accumulated by halophilic bacteria isolated from solar salterns.

Methods and Results

Twenty‐six halophilic isolates were obtained from solar salterns of Goa, India. They were screened for accumulation of PHA by Sudan black B, Nile blue A and Nile red stains. Strains H15, H16 and H26 were selected based on their intensity of Nile blue A/Nile red fluorescence. On the basis of phenotypic and genotypic characterization, the three isolates were identified as Bacillus megaterium. Growth kinetics and polymer accumulating capacity of strain H16 were studied in E2 mineral media with 2% glucose with/without NaCl. In the absence of NaCl, strain H16 accumulated PHA to 40·0% (w/w) of cell dry weight (CDW) at 42 h of growth, whereas in presence of 5% w/v NaCl, the culture showed longer lag phase of up to 24 h and accumulated a maximum PHA of 39% (w/w) CDW at 54 h of growth. The infrared spectra of both the polymers exhibited peaks at 1733·9 cm^?1 characteristic of C=O. Scans of ¹H nuclear magnetic resonance (NMR) showed a doublet at 2·5 ppm corresponding to methylene group (‐CH₂), the signal at 5·3 ppm corresponded to methine group (‐CH‐), and another signal at 1·3 ppm corresponded to the methyl group (‐CH₃). Scans of ¹³C NMR showed prominent peaks at 20, 40, 67–68 and 170 ppm, indicating the polymer to be homopolymer of 3‐hydroxybutyrates. The polymer is stable up to a temperature of 160°C.

Conclusion

Three moderately halophilic isolates (strain H15, H16 and H26) capable of accumulating PHA were isolated from solar salterns of Ribandar Goa, India, and identified as B. megaterium based on phenotypic and genotypic characterization. Strain H16 accumulated polyhydroxybutyrate in the presence and absence of NaCl up to 40% of its CDW.

Significance and Impact of the Study

This strain would be better suited for production of PHA at industrial level due to its tolerance to high concentration of NaCl.     

High resolution 13C NMR spectra on oriented lipid bilayers: from quantifying the various sources of line broadening to performing 2D experiments with 0.2-0.3 ppm resolution in the carbon dimension

¹³C NMR spectra routinely performed on oriented lipid bilayers display linewidth of 1–2 ppm, although T₂ measurements indicate that 0.1–0.2 ppm could be obtained. We have prepared a DMPC – ¹³C₄-cholesterol (7/3) sample, and oriented the lipid bilayers between glass plates so that the bilayer normal makes an angle of 90° (or of the magic angle) with B₀. We have measured T₂s, CSAs, and linewidths for the choline ¹³C--methyl, the cholesterol-C₄ carbons and the lipid head group phosphorus, at both angles and 313 K. The magnetic field distribution within the sample was calculated using the surface current formalism. The line shapes were simulated as a function of B₀ field inhomogeneities and sample mosaic spread. Both effects contribute to the experimental linewidth. Using three signals of different CSA, we have quantified both contributions and measured the mosaic spread accurately. Direct shimming on a sample signal is essential to obtain sharp resonances and ¹³C labelled choline methyl resonance of DMPC is a good candidate for this task. After optimisation of the important parameters (shimming on the choline resonance, mosaic spread of ±0.30° ), ¹³C linewidth of 0.2–0.3 ppm have been obtained. This newly achieved resolution on bilayers oriented at 90°, has allowed to perform two 2D experiments, with a good sensitivity: 2D PELF (correlation of carbon chemical shifts and C-H dipolar couplings) and 2D D-resolved experiment (correlation of carbon chemical shifts and C-C dipolar couplings). A C-C dipolar coupling of 35 ± 2 Hz between the choline methyl carbons was determined.     

Study of Pt(II)-aromatic amines complexes of the types cis- and trans-Pt(amine)2I2, [Pt(amine)4]I2 and I(amine)Pt(μ-I)2Pt(amine)I

Pt(II) complexes of the types cis- and trans-Pt(amine)₂I₂ with amines containing a phenyl group were synthesized and studied mainly by IR and multinuclear (¹⁹⁵Pt, ¹H and ¹³C) magnetic resonance spectroscopies. The compounds are not very soluble. In ¹⁹⁵Pt NMR spectroscopy, the cis isomers were observed at slightly lower fields than the trans analogues (average Δδ = 11 ppm) in acetone. In ¹H NMR, the NH groups were also found at slightly lower fields in the cis isomers. The coupling constants ²J(¹⁹⁵Pt-¹HN) varied from 53 to 85 Hz and seem slightly smaller in the trans configuration. The ¹³C NMR spectra of most of the complexes were measured. No coupling constants J(¹⁹⁵Pt-¹³C) were detected due to the low solubility of the compounds. The cis isomers containing a phenyl group on the N atom could not be isolated except for Ph-NH₂ which was shown to be a mixture of isomers in acetone. The tetrasubstituted ionic compounds [Pt(amine)₄]I₂ for the less crowded ligands were also studied mainly by NMR spectroscopy in aqueous solution. The ¹⁹⁵Pt chemical shifts vary between −2855 and −2909 ppm. The coupling constants ³J(¹⁹⁵Pt-¹H) are about 40 Hz. The iodo-bridged dinuclear species I(amine)Pt(μ-I)₂Pt(amine)I were also synthesized and characterized. Two isomers are present in acetone solution for most of the compounds. Their δ(Pt) signals were observed at about −4000 ppm and their coupling constants ²J(¹⁹⁵Pt-¹HN) are around 69 Hz.     

M1 Muscarinic Receptors Contribute to, whereas M4 Receptors Inhibit, Dopamine D1 Receptor-Induced [3H]-Cyclic AMP Accumulation in Rat Striatal Slices

In rat striatal slices labelled with [³H]-adenine and in the presence of 1 mM 3-isobutyl-1-methylxantine (IBMX), cyclic [³H]-AMP ([³H]-cAMP) accumulation induced by the dopamine D₁ receptor agonist SKF-81297 (1 μM; 177±13% of basal) was inhibited by the general muscarinic agonist carbachol (maximum inhibition 72±3%, IC₅₀ 0.30±0.06 μM). The muscarinic toxin 7 (MT-7), a selective antagonist at muscarinic M₁ receptors, reduced the effect of SKF-81297 by 40±7% (IC₅₀ 251±57 pM) and enhanced the inhibitory action of a submaximal (1 μM) concentration of carbachol (69±4% vs. 40±7% inhibition, IC₅₀ 386±105 pM). The toxin MT-1, agonist at M₁ receptors, stimulated [³H]-cAMP accumulation in a modest but significant manner (137±11% of basal at 400 nM), an action additive to that of D₁ receptor activation and blocked by MT-7 (10 nM). The effects of MT-7 on D₁ receptor-induced [³H]-cAMP accumulation and the carbachol inhibition were mimicked by the PKC inhibitors Ro-318220 (200 nM) and Gö-6976 (200 nM). Taken together our results indicate that in addition to the inhibitory role of M₄ receptors, in rat striatum acetylcholine stimulates cAMP formation through the activation of M₁ receptors and PKC stimulation.     

Multinuclear magnetic resonance study of Pt(II) compounds with sulfoxide ligands and crystal structures of complexes of the types [Pt(R2SO)X3] and Pt(R2SO)2Cl2

Pt(II) complexes of the types K[Pt(R₂SO)X₃], NR₄[Pt(R₂SO)X₃] and Pt(R₂SO)₂Cl₂ (where X = Cl or Br) were characterized by multinuclear magnetic resonance spectroscopy (¹⁹⁵Pt, ¹H and ¹³C). In ¹⁹⁵Pt NMR, the chloro ionic compounds have shown signals between −2979 and −3106 ppm, while the cis disubstituted complexes were observed at higher fields, between −3450 and −3546 ppm. The signal of the compound trans-Pt(DPrSO)₂Cl₂ was found at higher field (−3666 ppm) than its cis analogue (−3517 ppm), since π-back-donation is considerably less effective in the trans geometry. In ¹H NMR, a single signal was observed for the sulfoxide in [Pt(DMSO)Cl₃]⁻, but for the other more sterically hindered ligands, two series of resonances were observed for the protons in α and β positions. The coupling constant ³J(¹⁹⁵Pt-¹H) are between 15 and 33 Hz. The ¹³C NMR results were interpreted in relation to the concept of inversed polarization of the π sulfoxide bond. The ²J(¹⁹⁵Pt-¹³C) values vary between 35 and 66 Hz, while a few ³J(¹⁹⁵Pt-¹³C) couplings were observed (13-26 Hz). The crystal structures of five monosubstituted ionic compounds N(n-Bu)₄[Pt(TMSO)Cl₃], N(Me)₄[Pt(DPrSO)Cl₃], K[Pt(EMSO)Cl₃], K[Pt(TMSO)Br₃] · H₂O and N(Et)₄[Pt(DPrSO)Br₃] and one disubstituted complex cis-Pt(DBuSO)₂Cl₂ were determined. The trans influence of the different ligands is discussed.     

Resolution enhanced homonuclear carbon decoupled triple resonance experiments for unambiguous RNA structural characterization

Large RNAs (>30 nucleotides) suffer from extensive resonance overlap that can seriously hamper unambiguous structural characterization. Here we present a set of 3D multinuclear NMR experiments with improved and optimized resolution and sensitivity for aiding with the assignment of RNA molecules. In all these experiments strong base and ribose carbon–carbon couplings are eliminated by homonuclear band-selective decoupling, leading to improved signal to noise and resolution of the C5, C6, and C1′ carbon resonances. This decoupling scheme is applied to base-type selective ¹³C-edited NOESY, ¹³C-edited TOCSY (HCCH, CCH), HCCNH, and ribose H1C1C2 experiments. The 3D implementation of the HCCNH experiment with both carbon and nitrogen evolution enables direct correlation of ¹³C and ¹⁵N resonances at different proton resonant frequencies. The advantages of the new experiments are demonstrated on a 36 nucleotides hairpin RNA from domain 5 (D5) of the group II intron Pylaiella littoralis using an abbreviated assignment strategy. These four experiments provided additional separation for regions of the RNA that have overlapped chemical shift resonances, and enabled the assignment of critical D5 bulge nucleotides that could not be assigned using current experimental schemes.Supplementary material to this paper is available in electronic form at http://dx.doi.org/10.1007/s10858-005-5093-6     

Mycosporine-like amino acids in azooxanthellate and zooxanthellate early developmental stages of the soft coral Heteroxenia fuscescens

The ontogenetic changes of MAAs in the soft coral Heteroxenia fuscescens was studied in relation to their symbiotic state (azooxanthellate vs. zooxanthellate) under different temperature conditions in the Gulf of Eilat, northern Red Sea. The HPLC chromatograms for extracts of the planulae, azoo- and zooxanthellate primary polyps of H. fuscescens from all dates of collection yielded a single peak at 320 nm that has been identified as the compound palythine. Concentration of palythine in planulae at 23 °C was 7.57 ± 1 nmol mg^− 1 protein and at 28 °C reached 17.29 ± 1 nmol × mg^− 1 protein. Concentration of palythine in azooxanthellate primary polyps was 16.4 ± 3 nmol × mg^− 1 protein and 28.37 ± 2.8 nmol × mg^− 1 protein at 23 °C and 28 °C respectively. The palythine concentration for zooxanthellate primary polyps at 23 °C was 13 ± 3 nmol × mg^− 1 protein and at 28 °C 32.7 ± 2 nmol mg^− 1 protein. Palythine concentrations were significantly higher at 28 °C in the different animal groups and correlated linearly with the ambient collection temperature. This study shows for the first time that UVR and temperature act synergistically and affect the MAA levels of early life-history stages of soft corals.     

A stable carbon isotope study of dissolved inorganic carbon cycling in a softwater lake

The dissolved inorganic carbon (DIC) cycle in a softwater lake was studied using natural variations of the stable isotopes of carbon,¹²C and¹³C. During summer stratification there was a progressive decrease in epilimnion DIC concentration with a concomitant increase in ¹³C_DIC), due to preferential uptake of¹²C by phytoplankton and a change in the dominant CO₂ source from inflow andin situ oxidation to invasion from the atmosphere. There was an increase in hypolimnion DIC concentration throughout summer with a concomitant general decrease in ¹³C_DIC from oxidation of the isotopically light particulate organic carbon that sank down through the thermocline from the epilimnion.Mass balance calculations of DI¹²C and DI¹³C in the epilimnion for the summer (June 23–September 25) yield a mean rate of net conversion of DIC to organic carbon (C_org) of 430 ± 150 moles d^-1 (6.5 ± 1.8 m moles m^-2 d^-1. Net CO₂ invasion from the atmosphere was 420 ± 120 moles d^-1 (6.2 ± 1.8 m moles m^-2 d^-1) with an exchange coefficient of 0.6 ± 0.3m d^-1. These results imply that at least for the summer months the phytoplankton obtained about 90% of their carbon from atmosphere CO₂. About 50% of CO₂ invasion and conversion to C_org for the summer occurred during a two week interval in mid-summer.DIC concentration increased in the hypolimnion at a rate of 350 ± 70 moles DIC d^-1 during summer stratification. The amount of DIC added to the hypolimnion was equivalent to 75 ± 20% of net conversion of DIC to C_org in the euphotic zone over spring and summer implying rapid degradation of POC in the hypolimnion. The ¹³C of DIC added to the deep water (-22.) was too heavy to have been derived from oxidation of particulate organic carbon alone. About 20% of the added DIC must have diffused from hypolimnetic sediments where relatively heavy CO₂ (-7) was produced by a combination of POC oxidation and as a by-product of methanogenesis.     

Ca2+-Dependent and Ca2+-Independent [3H]GABA Release from Rat Brain Synaptosomes: the Effect of Temperature

The main inhibitory neurotransmitter GABA in the mammalian brain is distributed in the nerve terminals between two pools, vesicular (synaptic vesicles) and cytosolic. GABA is released from these pools by different mechanisms; there are calcium-activated exocytotic release and calcium-independent sodium-dependent release from the cytosolic pool (resulting from the membrane GABA transporter reversal). We investigated the influence of temperature on [³H]GABA release from rat brain synaptosomes, which was induced by stimulation of both these processes. In addition, we used -latrotoxin as a stimulant of [³H]GABA release. Synaptosomes from the rat brain were used in the experiments. 4-Aminopyridine (4-AP) and high [KCl] were applied to stimulate calcium-activated and calcium-independent [³H]GABA release, respectively. 4-AP-evoked [³H]GABA release was of the same intensity at 37 and 25°C (10.1 ± 1.2 and 10.1 ± 0.8% of total [³H]GABA incorporated into the synaptosomes, respectively). The effect of 4-AP on the ⁴⁵Ca²⁺ influx into synaptosomes was also temperature-independent: 0.775 ± 0.075 and 0.725 ± 0.100 nmol/min/mg of protein at 37 and 25°C, respectively. A drop in the effect of 4-AP was observed only at 15°C. When synaptosomes were depolarized with 50 mM KCl, a temperature decrease from 37°C to 25°C resulted in a twofold drop in the [³H]GABA release, from 20.5 ± 1.4 to 10.3 ± 0.7%; at 15°C [³H]GABA release dropped to less than one-third of the norm (6.0 ± 0.5%). -Latrotoxin-stimulated [³H]GABA release was diminished from 32.5 ± 2.5 at 37°C to 17.2 ± 1.3 at 25°C and 5.9 ± 0.4% at 15°C and was not affected by the presence or absence of calcium in the medium. It seems likely that the observed effect of temperature can be interpreted as based on the temperature dependence of the -latrotoxin insertion into the membrane. It is suggested that the pattern of the temperature sensitivity of GABA release from the synaptosomes can be used as a criterion for identification of the mode of neurotransmitter release.     

Effect of deuteration on some structural parameters of methyl groups in proteins as evaluated by residual dipolar couplings

One bond methyl ¹H-¹³C and ¹³C_methyl–¹³C scalar and residual dipolar couplings have been measured at sites in an ¹⁵N, ¹³C, 50% ²H labeled sample of the B1 immunoglobulin binding domain of peptostreptococcal protein L to investigate changes in the structure of methyl groups in response to deuterium substitution. Both one bond methyl ¹H-¹³C and ¹³C_methyl–¹³C scalar coupling constants have been found to decrease slightly with increasing deuterium content. Previous studies have shown that ¹H-¹³C couplings in methyl groups are exquisitely sensitive to electronic structure, with decreases in coupling values as a function of deuteration consistent with a slight lengthening of the remaining H-C bonds. Changes in the H_methylC_methylC angle are found to be small, with average differences on the order of 0.3 ± 0.1° and 0.4 ± 0.2° between CH₃, CH₂D and CH₃, CHD₂ isotopomers, respectively. Knowledge of methyl geometry is a prerequisite for the extraction of accurate dynamics parameters from spin relaxation studies involving these groups.