Raman 18O-labeling of bacteria in visible and deep UV-ranges

Raman stable isotope labeling with ²H, ¹³C or ¹⁵N has been reported as an elegant approach to investigate cellular metabolic activity, which is of great importance to reveal the functions of microorganisms in native environments. A new strategy termed Raman ¹⁸O-labeling was developed to probe the metabolic activity of bacteria. Raman ¹⁸O-labeling refers to the combination of Raman microspectroscopy with ¹⁸O-labeling using H₂¹⁸O. At an excitation wavelength of 532 nm, the incorporation of ¹⁸O into the amide I group of proteins and DNA/RNA bases was observed in Escherichia coli cells, while for an excitation wavelength electronically resonant with DNA or aromatic amino acid absorption at 244 nm ¹⁸O assimilation was detected using chemometric tools rather than visual inspection. Raman ¹⁸O-labeling at 532 nm combined with 2D correlation analysis confirmed the assimilation of ¹⁸O in proteins and nucleic acids and revealed the growth strategy of E. coli cells; they underwent protein synthesis followed by nucleic acid synthesis. Independent cultural replicates at different incubation times corroborated the reproducibility of these results. The variations in spectral features of ¹⁸O-labeled cells revealed changes in physiological information of cells. Hence, Raman ¹⁸O-labeling could provide a powerful tool to identify metabolically active bacterial cells.     

Enhancing the stability of O-labeled peptides through removal of immobilized trypsin by ZipTips

Trypsin-catalyzed ¹⁸O labeling is increasingly used in shotgun proteomics for relative peptide/protein quantitation. However, precise quantitative measurements are often complicated by the instability of ¹⁸O-labeled peptides caused mainly by oxygen back-exchange. Although a number of attempts have been made to reduce or prevent oxygen back-exchange, there is still room for improvement. Here we demonstrate that the removal of immobilized trypsin by filtration using ZipTips can efficiently minimize oxygen back-exchange and enhance the stability of ¹⁸O-labeled peptides under various pH conditions. The ¹⁸O-labeled peptides processed by the approach were successfully separated by immobilized pH gradient–isoelectric focusing (IPG–IEF), and no marked decrease in the extent of labeling was observed. The results also demonstrated that there was no correlation between the extent of ¹⁸O labeling and molecular weight or isoelectric point (pI). The approach presented here is especially applicable to microscale samples. Its ability to generate stably ¹⁸O-labeled samples without back-exchange should expand the application scope of the ¹⁸O-labeling technique.     

Incorporation of Oxygen from Water into Toluene and Benzene during Anaerobic Fermentative Transformation

Toluene and benzene were anaerobically transformed and eventually mineralized in mixed methanogenic cultures. However, the source of oxygen for the initial oxidation step had been unknown, owing to the presence of both methanol and water. No exogenous electron acceptors other than carbon dioxide, toluene, and benzene were present in the defined mineral medium. Through the use of ¹⁸O-labeled water, the oxygen incorporated into the monoaromatic compounds was shown to come from water. The cresol from the toluene and the phenol from the benzene contained up to 8% ¹⁸O label after incubation in 9% ¹⁸O-labeled medium. Gas chromatography-mass spectrometry was used to detect the ¹⁸O-labeled aromatic metabolites.     

Synthesis of <Superscript>18</Superscript>O-labeled photosynthetically active chlorophylls at the 3- or 7-carbonyl group with high regioselectivity

The 3- and 7-formyl groups of chlorophyll-d (Chl-d) and bacteriochlorophyll-e (BChl-e), respectively, were regioselectively labeled with an isotopically stable oxygen-18 (¹⁸O) atom to give 3¹-¹⁸O-labeled Chl-d and 7¹-¹⁸O-labeled BChl-e (ca. 90% ¹⁸O) by exchanging the carbonyl oxygen atoms in the presence of acidic H₂ ¹⁸O (ca. 95% ¹⁸O). Another photosynthetically active chlorophyll, BChl-a possessing the 3-acetyl group was treated under similar acidic conditions to afford a trace amount of 3¹-¹⁸O-labeled BChl-a and further demetallated compound, the corresponding 3¹-¹⁸O-labeled bacteriopheophytin-a as the major product with 55% ¹⁸O-degree. The FT-IR spectra of ¹⁸O-(un)labeled chlorophylls in the solution and the solid states showed that the 3- and 7-carbonyl stretching vibration modes moved to about a 30-cm⁻¹ lower wavenumber by ¹⁸O-labeling at the 3¹- and 7¹-oxo moieties. In artificial chlorosome-like self-aggregates of BChl-e, the ¹⁸O-labeled 7-carbonyl stretching mode was completely resolved from the specially hydrogen-bonded 13-C=O stretching mode, evidently indicating no interaction of the 7-CHO with other functional groups in the supramolecules.     

18O-labeled proteome reference as global internal standards for targeted quantification by selected reaction monitoring-mass spectrometry

Selected reaction monitoring (SRM)-MS is an emerging technology for high throughput targeted protein quantification and verification in biomarker discovery studies; however, the cost associated with the application of stable isotope-labeled synthetic peptides as internal standards can be prohibitive for screening a large number of candidate proteins as often required in the preverification phase of discovery studies. Herein we present a proof of concept study using an (18)O-labeled proteome reference as global internal standards (GIS) for SRM-based relative quantification. The (18)O-labeled proteome reference (or GIS) can be readily prepared and contains a heavy isotope ((18)O)-labeled internal standard for every possible tryptic peptide. Our results showed that the percentage of heavy isotope ((18)O) incorporation applying an improved protocol was >99.5% for most peptides investigated. The accuracy, reproducibility, and linear dynamic range of quantification were further assessed based on known ratios of standard proteins spiked into the labeled mouse plasma reference. Reliable quantification was observed with high reproducibility (i.e. coefficient of variance <10%) for analyte concentrations that were set at 100-fold higher or lower than those of the GIS based on the light ((16)O)/heavy ((18)O) peak area ratios. The utility of (18)O-labeled GIS was further illustrated by accurate relative quantification of 45 major human plasma proteins. Moreover, quantification of the concentrations of C-reactive protein and prostate-specific antigen was illustrated by coupling the GIS with standard additions of purified protein standards. Collectively, our results demonstrated that the use of (18)O-labeled proteome reference as GIS provides a convenient, low cost, and effective strategy for relative quantification of a large number of candidate proteins in biological or clinical samples using SRM.     

A method to determine 18 O kinetic isotope effects in the hydrolysis of nucleotide triphosphates

A method to determine 18 O kinetic isotope effects (KIEs) in the hydrolysis of GTP that is generally applicable to reactions involving other nucleotide triphosphates is described. Internal competition, where the substrate of the reaction is a mixture of 18 O-labeled and unlabeled nucleotides, is employed, and the change in relative abundance of the two species in the course of the reaction is used to calculate KIE. The nucleotide labeled with 18 O at sites of mechanistic interest also contains 13C at all carbon positions, whereas the 16 O-labeled nucleotide is depleted of 13C. The relative abundance of the labeled and unlabeled substrates or products is reflected in the carbon isotope ratio (13C/12C) in GTP or GDP, which is determined by the use of a liquid chromatography-coupled isotope ratio mass spectrometer (LC-coupled IRMS). The LC is coupled to the IRMS by an Isolink interface. Carbon isotope ratios can be determined with accuracy and precision greater than 0.04% and are consistent over an order of magnitude in sample amount. KIE values for Ras/NF1(333)-catalyzed hydrolysis of [beta18 O3,13C]GTP were determined by change in the isotope ratio of GTP or GDP or the ratio of the isotope ratio of GDP to that of GTP. KIE values computed in the three ways agree within 0.1%, although the method using the ratio of isotope ratios of GDP and GTP gives superior precision (<0.1%). A single KIE measurement can be conducted in 25 min with less than 5 microg nucleotide reaction product.     

18O Labeling of Chlorophyll d in Acaryochloris marina Reveals That Chlorophyll a and Molecular Oxygen Are Precursors

The cyanobacterium Acaryochloris marina was cultured in the presence of either H₂¹⁸O or ¹⁸O₂, and the newly synthesized chlorophylls (Chl a and Chl d) were isolated using high performance liquid chromatography and analyzed by mass spectroscopy. In the presence of H₂¹⁸O, newly synthesized Chl a and d, both incorporated up to four isotopic ¹⁸O atoms. Time course H₂¹⁸O labeling experiments showed incorporation of isotopic ¹⁸O atoms originating from H₂¹⁸O into Chl a, with over 90% of Chl a ¹⁸O-labeled at 48 h. The incorporation of isotopic ¹⁸O atoms into Chl d upon incubation in H₂¹⁸O was slower compared with Chl a with ∼50% ¹⁸O-labeled Chl d at 115 h. The rapid turnover of newly synthesized Chl a suggested that Chl a is the direct biosynthetic precursor of Chl d. In the presence of ¹⁸O₂ gas, one isotopic ¹⁸O atom was incorporated into Chl a with approximately the same kinetic incorporation rate observed in the H₂¹⁸O labeling experiment, reaching over 90% labeling intensity at 48 h. The incorporation of two isotopic ¹⁸O atoms derived from molecular oxygen (¹⁸O₂) was observed in the extracted Chl d, and the percentage of double isotopic ¹⁸O-labeled Chl d increased in parallel with the decrease of non-isotopic-labeled Chl d. This clearly indicated that the oxygen atom in the C3¹-formyl group of Chl d is derived from dioxygen via an oxygenase-type reaction mechanism.     

Oxygen Isotope Exchange between Metabolites and Water during Biochemical Reactions Leading to Cellulose Synthesis

Cellulose was produced heterotrophically from different carbon substrates by carrot tissue cultures and Acetobacter xylinum (a cellulose-producing bacterium) and by castor bean seeds germinated in the dark, in each case in the presence of water having known concentration of oxygen-18 (¹⁸O). We used the relationship between the amount of ¹⁸O in the water and in the cellulose that was synthesized to determine the number and ¹⁸O content of the substrate oxygens that exchanged with water during the reactions leading to cellulose synthesis. Our observations support the hypothesis that oxygen isotope ratios of plant cellulose are determined by isotopic exchange occurring during hydration of carbonyl groups of the intermediates of cellulose synthesis.     

Variations in the natural abundance of oxygen-18 and deuterium in plant carbohydrates

Variations in the natural abundance of ¹⁸O and ²H in plant cellulose are influenced by the isotopic composition of the water directly involved in metabolism—the metabolic water fraction. The isotopic distinction between the metabolic source water and total tissue water must reflect the formation of isotopic gradients within the tissue that are influenced by the rate of water turnover, by properties of the water conducting system and by environmental conditions. It seems that the ¹⁸O abundance in the metabolic water is conserved in cellulose with a relatively constant isotope effect. The relationship of the ²H abundance between metabolic water and cellulose is more complex. Hydrogen incorporated into photosynthetic products during primary reduction steps is highly depleted in ²H. However, a large proportion of these hydrogens are subsequently replaced by exchange with water, leading to ²H enrichment during heterotrophic metabolism. Deciphering the oxygen isotope ratio of cellulose could help in providing insights into the carbon and oxygen fluxes exchanged between plants and the atmosphere. This is because the ¹⁸O abundance in cellulose records the ¹⁸O abundance in the metabolic water, which in turn, controls the oxygen isotopic signatures of the CO₂ and O₂ released by plants into the atmosphere. The hydrogen isotope effects associated with carbohydrate metabolism provide insights into the autotrophic state of a plant tissue. This is because the hydrogen isotope ratio of carbohydrates must reflect the net effects of the two opposing isotope effects associated with photosynthesis and heterotrophic metabolism.     

Glycolate Metabolism in Low and High CO(2)-Grown Chlorella pyrenoidosa and Pavlova lutheri as Determined by O-Labeling

Photorespiration in Chlorella pyrenoidosa Chick. was assayed by measuring ¹⁸O-labeled intermediates of the glycolate pathway. Glycolate, glycine, serine, and excreted glycolate were isolated and analyzed on a gas chromatograph/mass spectrometer to determine isotopic enrichment. Rates of glycolate synthesis were determined from ¹⁸O-labeling kinetics of the intermediates, pool sizes, derived rate equations, and nonlinear regression techniques. Glycolate synthesis was higher in high CO₂-grown cells than in air-grown cells when both were assayed under the same O₂ and CO₂ concentrations. Synthesis of glycolate, for both types of cells, was stimulated by high O₂ levels and inhibited by high CO₂ levels. Glycolate synthesis in 1.5% CO₂-grown Chlorella, when exposed to a 0.035% CO₂ atmosphere, increased from about 41 to 86 nanomoles per milligram chlorophyll per minute when the O₂ concentration was increased from 21% to 40%. Glycolate synthesis in air-grown cells increased from 2 to 6 nanomoles per milligram chlorophyll per minute under the same gas levels. Synthesis was undetectable when either the O₂ concentration was lowered to 2% or the CO₂ concentration was raised to 1.5%. Glycolate excretion was also sensitive to O₂ and CO₂ concentrations in 1.5% CO₂-grown cells and the glycolate that was excreted was ¹⁸O-labeled. Air-grown cells did not excrete glycolate under any experimental condition. Indirect evidence indicated that glycolate may be excreted as a lactone in Chlorella. Photorespiratory ¹⁸O-labeling kinetics were determined for Pavlova lutheri, which unlike Chlorella and higher plants did not directly synthesize glycine and serine from glycolate. This alga did excrete a significant proportion of newly synthesized glycolate into the media.     

Optimization and quality assessment of the post-digestion O labeling based on urea for protein denaturation by HPLC/ESI-TOF mass spectrometry

The post-digestion ¹⁸O labeling method decouples protein digestion and peptide labeling. This method allows labeling conditions to be optimized separately and increases labeling efficiency. A common method for protein denaturation in proteomics is the use of urea. Though some previous studies have used urea-based protein denaturation before post-digestion ¹⁸O labeling, the optimal ¹⁸O labeling conditions in this case have not been yet reported. Present study investigated the effects of urea concentration and pH on the labeling efficiency and obtained an optimized protocol. It was demonstrated that urea inhibited ¹⁸O incorporation depending on concentration. However, a urea concentration between 1 and 2 M had minimal effects on labeling. It was also demonstrated that the use of FA to quench the digestion reaction severely affected the labeling efficiency. This study revealed the reason why previous studies gave different optimal pH for labeling. They neglect the effects of different digestion conditions on the labeling conditions. Excellent labeling quality was obtained at the optimized conditions using urea 1–2 M and pH 4.5, 98.4 ± 1.9% for a standard protein mixture and 97.2 ± 6.2% for a complex biological sample. For a 1:1 mixture analysis of the ¹⁶O- and ¹⁸O-labeled peptides from the same protein sample, the average abundance ratios reached 1.05 ± 0.31, demonstrating a good quantitation quality at the optimized conditions. This work will benefit other researchers who pair urea-based protein denaturation with a post-digestion ¹⁸O labeling method.     

Spatial and temporal trends in stable carbon and oxygen isotope ratios of juvenile winter flounder otoliths

Isotopic ratios of fish otoliths have been used in numerous studies as natural tags or markers to aid in the study of connectivity among fish populations. We investigated the use of spatial and temporal changes in the stable carbon and oxygen isotope ratios of otoliths to differentiate juvenile habitats of winter flounder (Pseudopleuronectes americanus). Young-of-the-year (YOY) juvenile winter flounder were collected annually over a three-year period from 18 stations along the coast of Rhode Island, USA. Sagittal otoliths were removed from fish and analyzed for stable carbon (¹³C/¹²C or δ¹³C) and oxygen (¹⁸O/¹⁶O or δ¹⁸O) isotope ratios using continuous flow isotope ratio mass spectrometry. Differences in isotope ratios were observed among stations and along salinity gradients in the Narragansett Bay estuary and an estuarine river system (Narrow River). Overall, the isotope ratio patterns observed among stations were consistent over the three sampling years; however, differences were noted in isotope ratios and the magnitude of the isotope ratio gradients among years. Significant positive correlations were noted between salinity and δ¹³C for two of the three years. For each of the three years sampled there was a highly significant positive correlation (2002, r = 0.93, P < 0.01; 2003, r = 0.85, P < 0.01; 2004, r = 0.97, P < 0.01) between δ¹⁸O and the salinity of the collection site. Also, there was a significant negative correlation between the number of months of above average river flow and δ¹⁸O for the three sampling years (r = 0.99, P < 0.05). These findings suggest that yearly changes in the volume of freshwater inputs to these estuarine habitats may be related to the differences observed in otolith δ¹⁸O isotope ratios. Because of these year-to-year differences, sampling of each cohort may be necessary in order to use this isotopic technique for winter flounder connectivity studies.     

Conformational changes of recombinant monoclonal antibodies by limited proteolytic digestion,stable isotope labeling,and liquid chromatography–mass spectrometry

Limited proteolytic digestion is a method with a long history that has been used to study protein domain structures and conformational changes. A method of combining limited proteolytic digestion, stable isotope labeling, and mass spectrometry was established in the current study to investigate protein conformational changes. Recombinant monoclonal antibodies with or without the conserved oligosaccharides, and with or without oxidation of the conserved methionine residues, were used to test the newly proposed method. All of the samples were digested in ammonium bicarbonate buffer prepared in normal water. The oxidized deglycosylated sample was also digested in ammonium bicarbonate buffer prepared in ¹⁸O-labeled water. The sample from the digestion in ¹⁸O–water was spiked into each sample digested in normal water. Each mixed sample was subsequently analyzed by liquid chromatography–mass spectrometry (LC–MS). The molecular weight differences between the peptides digested in normal water versus ¹⁸O–water were used to differentiate peaks from the samples. The relative peak intensities of peptides with or without the C-terminal incorporation of ¹⁸O atoms were used to determine susceptibility of different samples to trypsin and chymotrypsin. The results demonstrated that the method was capable of detecting local conformational changes of the recombinant monoclonal antibodies caused by deglycosylation and oxidation.     

Reconstruction of source water using the δ18O of tree ring phenylglucosazone: A potential tool in paleoclimate studies

The oxygen isotope ratios of tree ring cellulose have a great potential as proxy for the oxygen isotope ratios of source water, which is related to climate. However, source water isotopic signatures can be masked by plant physiological and biochemical processes during cellulose synthesis. To minimize biochemical effects in the recording of source water, we modified the cellulose molecule to phenylglucosazone, which only has oxygen attached to carbon 3–6 (O_C3–6) of the cellulose glucose moieties, thus eliminating the oxygen attached to carbon 2 of the cellulose glucose moieties (O_C-2). Here we developed a method to use small amounts of inter and intra-annual tree ring cellulose for phenylglucosazone synthesis. Using this new method we tested if the oxygen isotope ratios of source water reconstructed from tree ring phenylglucosazone (δ¹⁸O_sw^PG) and the observed source water (δ¹⁸O_sw^obs) would have a better agreement than those reconstructed from the tree ring cellulose molecule. Annual tree ring samples were obtained from Pinus sylvestris (1997–2003) (Finland) and Picea abies (1971–1992) (Switzerland) and intra-annual tree ring samples were obtained from Pinus radiata (October 2004–March 2006) (New Zealand), each near a meteorological station where precipitation and relative humidity (RH) were measured periodically. The δ¹⁸O of tree ring cellulose and tree ring phenylglucosazone for each of the three species were then used to back calculate the δ¹⁸O of source water according to a previous published empirical equation. As expected, the δ¹⁸O of tree ring phenylglucosazone was superior than cellulose in the reconstruction of source water available to the plant. Deviation between δ¹⁸O_sw^PG and δ¹⁸O_sw^obs was in part correlated with variation in atmospheric relative humidity (RH) which was not observed for the cellulose molecule. We conclude that this new method can be applicable to inter and intra-annual tree ring studies and that the use of the tree ring phenylglucosazone will significantly improve the quality of paleoclimate studies.     

Stable isotope analysis of modern human hair collected from Asia (China,India, Mongolia,and Pakistan)

We report isotopic data (δ²H, δ¹⁸O n = 196; δ¹³C, δ¹⁵N n = 142; δ³⁴S n = 85) from human hair and drinking water (δ²H, δ¹⁸O n = 67) collected across China, India, Mongolia, and Pakistan. Hair isotope ratios reflected the large environmental isotopic gradients and dietary differences. Geographic information was recorded in H and O and to a lesser extent, S isotopes. H and O data were entered into a recently developed model describing the relationship between the H and O isotope composition of human hair and drinking water in modern USA and pre‐globalized populations. This has anthropological and forensic applications including reconstructing environment and diet in modern and ancient human hair. However, it has not been applied to a modern population outside of the USA, where we expect different diet. Relationships between H and O isotope ratios in drinking water and hair of modern human populations in Asia were different to both modern USA and pre‐globalized populations. However, the Asian dataset was closer to the modern USA than to pre‐globalized populations. Model parameters suggested slightly higher consumption of locally producedfoods in our sampled population than modern USA residents, but lower than pre‐globalized populations. The degree of in vivo amino acid synthesis was comparable to both the modern USA and pre‐globalized populations. C isotope ratios reflected the predominantly C₃‐based regional agriculture and C₄ consumption in northernChina. C, N, and S isotope ratios supported marine food consumption in some coastal locales. N isotope ratios suggested a relatively low consumption of animal‐derived products compared to western populations. Am J Phys Anthropol 2010. © 2009 Wiley‐Liss, Inc.     

Frequency of N-benzyladenine incorporation into major RNA fractions of tobacco cell suspensions grown at stimulatory or cytostatic cytokinin concentration

The frequency of incorporation of the cytokinin N⁶-[p-³H]benzyladenine into major RNA species of tobacco (Nicotiana tabacum cv W 38) cells steadily increased as a function of its concentration in the culture medium, up to a 10 micromolar cytostatic overdose. During a 55-hour incubation of cells with 0.4 micromolar benzyladenine (BA), which is the optimal concentration for cell division, the incorporation frequency increased to one BA per 1.5 to 2.0 × 10⁴ conventional bases in total RNA. Frequencies of BA incorporation into 18S and 25S rRNA and into RNA precursors were very similar, 2- to 3-fold higher than the frequency of BA incorporation into the 4S + 5S RNA fraction. In cells incubated with 10 micromolar BA, the rate of RNA synthesis between 24 and 55 hours was lower than at optimal growth conditions; 18S and 25S rRNA synthesis was depressed more than the synthesis of 4S + 5S RNA. At 55 hours, BA was incorporated into total RNA at the steady state frequency of one per 1,300 conventional bases. All major RNA species were BA-labeled to approximately the same level, except that the labeling of the RNA precursors was 2-fold higher than the labeling of mature RNA species. These results may reflect an alteration in the processing of the RNA precursors at supra-optimal cytokinin concentration.     

Microderivatization of 4-[O]hydroxyproline and quantitation with a benchtop mass spectrometer

Accurate estimation of in vivo turnover rates of collagen is complicated by amino acid reutilization. It was previously shown that the ideal, non-recycling tracer was [¹⁸O]hydroxyproline synthesized in vivo. The analytical method for measuring turnover rates with [¹⁸O]hydroxyproline must include analyte quantitation for pool size determination and isotope ratio measurement for determining levels of label incorporation. For ease of use and widest availability, a benchtop gas chromatograph—mass spectrometer in the electron-impact ionization mode was chosen. Here we present a versatile procedure for hydroxyproline derivatization that is well suited for routine, large-scale determination of analyte concentrations and relative levels of ¹⁸O incorporation.     

Quantitative Microbial Ecology through Stable Isotope Probing

Bacteria grow and transform elements at different rates, and as yet, quantifying this variation in the environment is difficult. Determining isotope enrichment with fine taxonomic resolution after exposure to isotope tracers could help, but there are few suitable techniques. We propose a modification to stable isotope probing (SIP) that enables the isotopic composition of DNA from individual bacterial taxa after exposure to isotope tracers to be determined. In our modification, after isopycnic centrifugation, DNA is collected in multiple density fractions, and each fraction is sequenced separately. Taxon-specific density curves are produced for labeled and nonlabeled treatments, from which the shift in density for each individual taxon in response to isotope labeling is calculated. Expressing each taxon''s density shift relative to that taxon''s density measured without isotope enrichment accounts for the influence of nucleic acid composition on density and isolates the influence of isotope tracer assimilation. The shift in density translates quantitatively to isotopic enrichment. Because this revision to SIP allows quantitative measurements of isotope enrichment, we propose to call it quantitative stable isotope probing (qSIP). We demonstrated qSIP using soil incubations, in which soil bacteria exhibited strong taxonomic variations in ¹⁸O and ¹³C composition after exposure to [¹⁸O]water or [¹³C]glucose. The addition of glucose increased the assimilation of ¹⁸O into DNA from [¹⁸O]water. However, the increase in ¹⁸O assimilation was greater than expected based on utilization of glucose-derived carbon alone, because the addition of glucose indirectly stimulated bacteria to utilize other substrates for growth. This example illustrates the benefit of a quantitative approach to stable isotope probing.     

Incorporation of 13C,15N-labeled nucleosides and measurement of RNA synthesis and turnover in sea urchin embryos

The uptake of nucleosides into sea urchin embryos and their subsequent incorporation into RNA increases with increasing external nucleoside concentration. When embryos are incubated with high concentrations of ¹³C,¹⁵N-labeled nucleosides, newly synthesized RNA becomes sufficiently labeled with heavy isotope to be separated from unlabeled RNA on cesium formate equilibrium gradients. High concentrations of nucleosides do not affect development of embryos or rates of RNA synthesis. The extent of density-labeling of precursor pools increases with incubation time, and only levels off after many hours. During incubations with high concentrations of nucleosides, ATP pools expand up to twofold. Using density-labeling to circumvent precursor pool measurements, a method is presented to study the synthesis and decay of pulse-labeled RNA. The instantaneous rate of synthesis of total RNA at the blastula stage is 9.3 × 10^?15 mol of total nucleotide/embryo per minute and the average half-life of total RNA is 23 minutes.     

Determination of H-enrichment of rat brain interstitial fluid and rat plasma by headspace-gas-chromatography – quadrupole-mass-spectrometry

²H₂O as nonradioactive, stable marker substance is commonly used in preclinical and clinical studies and the precise determination of ²H₂O concentration in biological samples is crucial. However, aside from isotope ratio mass spectrometry (IRMS), only a very limited number of methods to accurately measure the ²H₂O concentration in biological samples are routinely established until now.