13C标记代谢流分析中天然稳定性同位素修正矩阵构建方法及应用

稳定性同位素¹³C标记实验是分析细胞代谢流的一种重要手段,主要通过质谱检测胞内代谢物中¹³C标记的同位素分布,并作为胞内代谢流计算时的约束条件,进而通过代谢流分析算法得到相应代谢网络中的通量分布。然而在自然界中,并非只有C元素存在天然稳定性同位素¹³C,其他元素如O元素也有其天然稳定性同位素¹⁷O、¹⁸O等,这使得质谱方法所测得的同位素分布中会夹杂除¹³C标记之外的其他元素的同位素信息,特别是分子中含有较多其他元素的分子,这将导致很大的实验误差,因此需要在进行代谢流计算前进行质谱数据的矫正。本研究提出了一种基于Python语言的天然同位素修正矩阵的构建方法,用于修正同位素分布测量值中由于天然同位素分布引起的测定误差。文中提出的基本修正矩阵幂方法用于构建各元素修正矩阵,结构简单、易于编码实现,可直接应用于¹³C代谢流分析软件数据前处理。将该修正方法应用于¹³C标记的黑曲霉（Aspergillus niger）胞内代谢流分析,结果表明本研究提出的方法准确有效,为准确获取微生物胞内代谢流分析提供了可靠的数据修正方法。     

Sensitive automated methods for phosphate and (Na+ plus K+)-ATPase

Sensitive automated methods for phosphate and (Na⁺ + K⁺)-ATPase are presented. The automated systems use sampler and pump modules from a Technicon autoanalyzer along with a Gilford spectrophotometer. The phosphate assay has a molar absorbance of approximately 87,000 m^?1 cm^?1 640 nm. The method uses a single color reagent and has been used successfully with perchloric acid digests of phospholipids.The (Na⁺ + K⁺)-ATPase method is based on the phosphate method. The method is comparable to manual methods in the amount of ATP and enzyme used per assay. The blank due to ATP is low. The precision of the assay on replicate samples is usually within ±1%. The total time delay for a single assay is less than 9 min and the method can be operated at a rate of 30 samples/hr. The method has been particularly useful in enzyme purification work. Procedures for the use of the method in kinetic studies are described     

Measurement of CO(2) Assimilation in Soils: an Experiment for the Biological Exploration of Mars

A method is described for the measurement of ¹⁴CO₂ assimilation by microorganisms in soils. A determination involves exposing soil to ¹⁴CO₂, pyrolyzing the exposed soil, trapping the organic pyrolysis products on a column of firebrick coated with CuO, combusting the trapped organics by heating, and measuring the radioactivity in the CO₂ produced in the combustion. The detection of significant levels of ¹⁴C in the trapped organic fraction appears to be an unambiguous indication of biological activity. The ¹⁴CO₂ which is adsorbed or exchanged into soils by nonbiological processes does not interfere. The method easily detects the ¹⁴CO₂ fixed by 10² to 10³ algae after light exposure for 3 to 24 hr. Assimilation of ¹⁴C is also demonstrable in dark-exposed soils containing 10⁵ to 10⁶ heterotrophic bacteria. Possible applications of the method in the biological exploration of Mars are discussed.     

Nitrification Rates in the Baltic Sea: Comparison of Three Isotope Techniques

Simultaneous measurements of nitrification in the Baltic Sea were made at 10- to 30-m intervals in the months of June and November by three isotope techniques: [¹⁵N]nitrate dilution, N-serve sensitive [¹⁴C]bicarbonate incorporation, and [¹⁵N]ammonium oxidation to nitrite and nitrate. Nitrification rates of 1 to 280 nmol liter⁻¹ day⁻¹ were recorded, and each method showed that the highest rates of nitrification occurred below the halocline. Even in the presence of ammonium, dark incubations of mixed layer (above ca. 50 m) waters never yielded nitrification rates exceeding 45 nmol liter⁻¹ day⁻¹. The rates measured by the ammonium oxidation method were two- to sevenfold greater than those obtained by ¹⁴C incorporation or ¹⁵N dilution. The merits of each technique are discussed, and it is suggested that the [¹⁵N]ammonium oxidation method should be used in conjunction with the [¹⁴C]bicarbonate incorporation method.     

Comparison Between Different Assays for Superoxide Dismutase-Like Activity

The direct and indirect methods for assaying the superoxide dismutase activity of a compound are compared. With the use of a direct method. the mechanism of the catalysis of O₂-dismutation by the tested compound can be determined. while with the indirect method it cannot. and this may lead to misinterpretation of the results. Assuming that the catalysis occurs via the ‘ping-pong’ mechanism, both the direct and indirect methods are limited to the determination of values of k_cat ≥ 10⁵M^?1s^?1 and k_cat ≥ 3 × 10⁶M^?1s^?1. respectively. Moreover, many side reactions may occur with the indirect method which may interfere with the measurements. Nevertheless. the indirect method approximates better the in vivo conditions than the direct method, and a tested compound that has high SOD activity using a direct method and low SOD activity using an indirect method. will most probably be a poor SOD mimic in vivo.     

Efficient fluorography of 3H and 14C on thin layers.

Three methods for efficient detection of ³H and ¹⁴C on thin layers are described. The first method uses 0.4% PPO dissolved in 2-methylnaphthalene. It is approximately 15-fold more efficient than 7% PPO-ether for ³H detection and 15-fold more efficient than autoradiography for ¹⁴C (or ³⁵S) detection. The second method uses PPO dissolved in ether. Efficiency of ³H detection increases as the PPO concentration is increased. The third method uses melted PPO and is as efficient as the first method when the film is exposed at ?78°C.     

Evaluation of automated analysis of 15N and total N in plant material and soil

Simultaneous determination of ¹⁵N and total N using an automated nitrogen analyser interfaced to a continuous-flow isotope ratio mass spectrometer (ANA-MS method) was evaluated. The coefficient of variation (CV) of repeated analyses of homogeneous standards and samples at natural abundance was lower than 0.1%. The CV of repeated analyses of ¹⁵N-labelled plant material and soil samples varied between 0.3% and 1.1%. The reproductibility of repeated total N analyses using the automated method was comparable to results obtained with a semi-micro Kjeldahl procedure. However, the automated method gave results which were 3% to 5% higher than those obtained with the Kjeldahl procedure. Since only small samples can be analysed, careful sample homogenization and fine grinding are very important. Evaluation of a diffusion method for preparing nitrate and ammonium in solution for automated ¹⁵N analysis showed that the recovery of inorganic N in the NH₃ trap was lower when the N was diffused from water than from 2 M KCl. The results also indicated that different proportions of the NO₃ ^- and the NH₄ ⁺ in aqueous solution were recovered in the trap after combined diffusion. The method is most suited for diffusing either NO₃ ^- or NH₄ ⁺ alone, but can be used for combined diffusion of the two ions.     

Improved Most-Probable-Number Method To Detect Sulfate-Reducing Bacteria with Natural Media and a Radiotracer

A greatly improved most-probable-number (MPN) method for selective enumeration of sulfate-reducing bacteria (SRB) is described. The method is based on the use of natural media and radiolabeled sulfate (³⁵SO₄²⁻). The natural media used consisted of anaerobically prepared sterilized sludge or sediment slurries obtained from sampling sites. The densities of SRB in sediment samples from Kysing Fjord (Denmark) and activated sludge were determined by using a normal MPN (N-MPN) method with synthetic cultivation media and a tracer MPN (T-MPN) method with natural media. The T-MPN method with natural media always yielded significantly higher (100- to 1,000-fold-higher) MPN values than the N-MPN method with synthetic media. The recovery of SRB from environmental samples was investigated by simultaneously measuring sulfate reduction rates (by a ³⁵S-radiotracer method) and bacterial counts by using the T-MPN and N-MPN methods, respectively. When bacterial numbers estimated by the T-MPN method with natural media were used, specific sulfate reduction rates (qSO₄²⁻) of 10⁻¹⁴ to 10⁻¹³ mol of SO₄²⁻ cell⁻¹ day⁻¹ were calculated, which is within the range of qSO₄²⁻ values previously reported for pure cultures of SRB (10⁻¹⁵ to 10⁻¹⁴ mol of SO₄²⁻ cell⁻¹ day⁻¹). qSO₄²⁻ values calculated from N-MPN values obtained with synthetic media were several orders of magnitude higher (2 × 10⁻¹⁰ to 7 × 10⁻¹⁰ mol of SO₄²⁻ cell⁻¹ day⁻¹), showing that viable counts of SRB were seriously underestimated when standard enumeration media were used. Our results demonstrate that the use of natural media results in significant improvements in estimates of the true numbers of SRB in environmental samples.     

Simple and rapid quantitative assay of C-labelled urea in human serum using liquid chromatography-atmospheric pressure chemical ionization mass spectrometry

A simple and rapid quantitative method for ¹³C-labelled urea ([¹³C]urea) in human serum was developed by using high-performance liquid chromatography-atmospheric pressure chemical ionization mass spectrometry (HPLC-APCI-MS). This method is used to establish and normalize the [¹³C]urea breath test, which is considered as an effective diagnostic method for Helicobacter pylori infection. HPLC-APCI-MS, involving a simple pretreatment process such as diluting serum with water, was shown to be able to discriminate the extrinsic [¹³C]urea from intrinsic urea present at high concentration in serum. In addition, a ¹³C nuclear magnetic resonance spectroscopic quantitative method for [¹³C]urea in human urine is also described. The precision and accuracy of measured concentrations in these two methods were found to be within the acceptable limit. An application of these methods to investigate the pharmacokinetic profile of orally administered [¹³C]urea in human serum and urine is also presented.     

Sub-Parts-Per-Billion Nitrate Method: Use of an N2O-Producing Denitrifier to Convert NO3− or 15NO3− to N2O

A more sensitive analytical method for NO₃⁻ was developed based on the conversion of NO₃⁻ to N₂O by a denitrifier that could not reduce N₂O further. The improved detectability resulted from the high sensitivity of the ⁶³Ni electron capture gas chromatographic detector for N₂O and the purification of the nitrogen afforded by the transformation of the N to a gaseous product with a low atmospheric background. The selected denitrifier quantitatively converted NO₃⁻ to N₂O within 10 min. The optimum measurement range was from 0.5 to 50 ppb (50 μg/liter) of NO₃⁻ N, and the detection limit was 0.2 ppb of N. The values measured by the denitrifier method compared well with those measured by the high-pressure liquid chromatographic UV method above 2 ppb of N, which is the detection limit of the latter method. It should be possible to analyze all types of samples for nitrate, except those with inhibiting substances, by this method. To illustrate the use of the denitrifier method, NO₃⁻ concentrations of <2 ppb of NO₃⁻ N were measured in distilled and deionized purified water samples and in anaerobic lake water samples, but were not detected at the surface of the sediment. The denitrifier method was also used to measure the atom% of ¹⁵N in NO₃⁻. This method avoids the incomplete reduction and contamination of the NO₃⁻ -N by the NH₄⁺ and N₂ pools which can occur by the conventional method of ¹⁵NO₃⁻ analysis. N₂O-producing denitrifier strains were also used to measure the apparent K_m values for NO₃⁻ use by these organisms. Analysis of N₂O production by use of a progress curve yielded K_m values of 1.7 and 1.8 μM NO₃⁻ for the two denitrifier strains studied.     

Validated spectrofluorimetric method for the determination of tamsulosin in spiked human urine,pure and pharmaceutical preparations

A novel, sensitive and selective spectrofluorimetric method was developed for the determination of tamsulosin in spiked human urine and pharmaceutical preparations. The proposed method is based on the reaction of tamsulosin with 1‐dimethylaminonaphthalene‐5‐sulfonyl chloride in carbonate buffer pH 10.5 to yield a highly fluorescent derivative. The described method was validated and the analytical parameters of linearity, limit of detection (LOD), limit of quantification (LOQ), accuracy, precision, recovery and robustness were evaluated. The proposed method showed a linear dependence of the fluorescence intensity on drug concentration over the range 1.22 × 10^‐7 to 7.35 × 10^‐6 M. LOD and LOQ were calculated as 1.07 × 10^‐7 and 3.23 × 10^‐7 M, respectively. The proposed method was successfully applied for the determination of tamsulosin in pharmaceutical preparations and the obtained results were in good agreement with those obtained using the reference method. Copyright © 2013 John Wiley & Sons, Ltd.     

A Novel Method for Relative Quantitation of N-Glycans by Isotopic Labeling Using 18O-Water

Quantitation is an essential aspect of comprehensive glycomics study. Here, a novel isotopic-labeling method is described for N-glycan quantitation using ¹⁸O-water. The incorporation of the ¹⁸O-labeling into the reducing end of N-glycans is simply and efficiently achieved during peptide-N4-(N-acetyl-β-glucosaminyl) asparagine amidase F release. This process provides a 2-Da mass difference compared with the N-glycans released in ¹⁶O-water. A mathematical calculation method was also developed to determine the ¹⁸O/¹⁶O ratios from isotopic peaks. Application of this method to several standard glycoprotein mixtures and human serum demonstrated that this method can facilitate the relative quantitation of N-glycans over a linear dynamic range of two orders, with high accuracy and reproducibility.     

Determination of Δ-tetrahydrocannabinol levels in brain tissue using high-performance liquid chromatography with electrochemical detection

Δ⁹-Tetrahydrocannabinol (Δ⁹-THC) is the major psychoactive component of cannabis. To assist in investigating the mechanism(s) of action of Δ⁹-THC, a convenient method for determining its levels in brain tissue is required. We now describe a method for determining nanogram quantities of Δ⁹-THC in rat brain tissue. The method employs solvent extraction with methanol-hexane-ethyl acetate, followed by analysis using liquid chromatography with electrochemical detection. Overall recoveries were greater than 80%. The relationship between the peak-height ratio for processed standards extracted in the presence of tissue (Δ⁹-THC/internal standard) and the amount of Δ⁹-THC added was shown to be linear within the range of concentrations examined. Quantitative measurements of Δ⁹-THC in different brain regions following the intravenous administration of Δ⁹-THC are presented as examples of the applications of this method.     

Comparison of the filtration and centrifugation methods for assaying [3H](d-ala2,d-leu5)enkephalin binding to mouse brain membranes

The binding of [³H](d-ala²,d-leu⁵)enkephalin (DADLE) to mouse brain membranes was studied via rapid filtration with GF/C filters and via the centrifugation method. The amount of specific binding determined by filtration was found to be dependent on the length of time between the initiation of vacuum and the actual time of filtration. Vacuum strength alone also significantly affected the amount of specifically bound [³H]DADLE measured by filtration. The centrifugation method increased the number of experimentally determined binding sites when compared to the filtration method. The difference in the number of binding sites was only partially attributable to passage of binding material through the GF/C filter. The ability of morphine to displace [³H]DADLE was also found to differ slightly between the two methods. These data indicate that centrifugation is a better method of determining the binding parameters of [³H]DADLE in mouse brain membrane preparations.     

High-Throughput Measurement and Classification of Organic P in Environmental Samples

Many types of organic phosphorus (P) molecules exist in environmental samples¹. Traditional P measurements do not detect these organic P compounds since they do not react with colorimetric reagents^2,3. Enzymatic hydrolysis (EH) is an emerging method for accurately characterizing organic P forms in environmental samples^4,5. This method is only trumped in accuracy by Phosphorus-31 Nuclear Magnetic Resonance Spectroscopy (³¹P-NMR) -a method that is expensive and requires specialized technical training⁶. We have adapted an enzymatic hydrolysis method capable of measuring three classes of phosphorus (monoester P, diester P and inorganic P) to a microplate reader system⁷. This method provides researchers with a fast, accurate, affordable and user-friendly means to measure P species in soils, sediments, manures and, if concentrated, aquatic samples. This is the only high-throughput method for measuring the forms and enzyme-lability of organic P that can be performed in a standard laboratory. The resulting data provides insight to scientists studying system nutrient content and eutrophication potential.     

Determination of isotope distribution in labeled lysine

A method is described for the degradation of ¹⁴C-labeled lysine with determination of radioactivity in the individual C atoms. The method depends on permanganate oxidation of lysine to give δ-aminopentanoic acid, γ-aminobutyric acid, β-alanine, and glycine, and on ninhydrin decarboxylation of glycine. The method will be equally useful for determining the distribution of ¹⁵N and ³H in lysine.     

A qualitative and quantitative HPTLC densitometry method for the analysis of cannabinoids in Cannabis sativa L.

Introduction – Cannabis and cannabinoid based medicines are currently under serious investigation for legitimate development as medicinal agents, necessitating new low‐cost, high‐throughput analytical methods for quality control. Objective – The goal of this study was to develop and validate, according to ICH guidelines, a simple rapid HPTLC method for the quantification of Δ⁹‐tetrahydrocannabinol (Δ⁹‐THC) and qualitative analysis of other main neutral cannabinoids found in cannabis. Methodology – The method was developed and validated with the use of pure cannabinoid reference standards and two medicinal cannabis cultivars. Accuracy was determined by comparing results obtained from the HTPLC method with those obtained from a validated HPLC method. Results – Δ⁹‐THC gives linear calibration curves in the range of 50–500 ng at 206 nm with a linear regression of y = 11.858x + 125.99 and r² = 0.9968. Conclusion – Results have shown that the HPTLC method is reproducible and accurate for the quantification of Δ⁹‐THC in cannabis. The method is also useful for the qualitative screening of the main neutral cannabinoids found in cannabis cultivars. Copyright © 2009 John Wiley & Sons, Ltd.     

Superoxide dismutase does not inhibit the oxidation of cytochrome c and cytochrome oxidase.

An electrometric system was used to measure Ca⁺⁺ uptake by sarcoplasmic reticulum vesicles (SR). The method permits continuous recording of Ca⁺⁺ uptake and thus the valuation of kinetic parameters. Furthermore, the ultrasensitivity of the method permits to follow changes in Ca⁺⁺ concentration below 10^?6 M.     

Double labeling of chromatin proteins,in vivo and in vitro,and their two-dimensional electrophoretic resolution

A modification of the two-dimensional electrophoretic method that involves nonequilibrium pH gradients has been adapted for high resolution of chromatin proteins from sea urchin embryos. A simple method of labeling the protein, in vitro, by reductive methylation with boro[³H]hydride to a specific activity of 100,000 cpm/μg of protein is detailed. Chromatin protein may be labeled, in vivo with ¹⁴C-amino acids, and newly synthesized (³H and ¹⁴C-labeled) and preexistent proteins (only ³H labeled) may be distinguished. The method reveals that sea urchin embryo chromatin contains over 200 proteins.     

Radiometric Method for the Detection of Coliform Organisms in Water

A new radiometric method for the detection of coliform bacteria in water has been described. The method is based on the release of ¹⁴CO₂ from [¹⁴C]lactose by bacteria suspended in growth medium and incubated at 37 C. The evolved ¹⁴CO₂ is trapped by hyamine hydroxide and counted in a liquid scintillation spectrometer. The method permits the detection of 1 to 10 organisms within 6 h of incubation. Coliform bacteria suspended in water for several days recover from starvation and may be quantitated by the proposed method. Bacteria from water samples may also be concentrated by filtration through membrane filters and detected by the radiometric assay.