Stable isotope ¹³C labeling is an important tool to analyze cellular metabolic flux. The ¹³C distribution in intracellular metabolites can be detected via mass spectrometry and used as a constraint in intracellular metabolic flux calculations. Then, metabolic flux analysis algorithms can be employed to obtain the flux distribution in the corresponding metabolic reaction network. However, in addition to carbon, other elements such as oxygen in the nature also have natural stable isotopes (e.g., ¹⁷O, ¹⁸O). This makes the isotopic information of elements other than the ¹³C marker interspersed in the isotopic distribution measured by the mass spectrometry, especially that of the molecules containing many other elements, which leads to large errors. Therefore, it is essential to correct the mass spectrometry data before performing metabolic flux calculations. In this paper, we proposed a method for construction of correction matrix based on Python language for correcting the measurement errors due to natural isotope distribution. The method employed a basic power method for constructing the correction matrix with simple structure and easy coding implementation, which can be directly applied to data pre-processing in ¹³C metabolic flux analysis. The correction method was then applied to the intracellular metabolic flux analysis of ¹³C-labeled Aspergillus niger. The results showed that the proposed method was accurate and effective, which can serve as a reliable data correction method for accurate microbial intracellular metabolic flux analysis.
Metabolic Flux Analysis ; Isotope Labeling/methods* ; Carbon Isotopes/metabolism* ; Mass Spectrometry/methods* ; Metabolic Networks and Pathways

¹³C metabolic flux analysis (¹³C-MFA) enables the precise quantification of intracellular metabolic reaction rates by analyzing the distribution of mass isotopomers of proteinogenic amino acids or intracellular metabolites through ¹³C labeling experiments. ¹³C-MFA has received much attention as it can help systematically understand cellular metabolic characteristics, guide metabolic engineering design and gain mechanistic insights into pathophysiology. This article reviews the advances of ¹³C-MFA in the past 30 years and discusses its potential and future perspective, with a focus on its application in industrial biotechnology and biomedicine.
Amino Acids ; Carbon Isotopes ; Isotope Labeling ; Metabolic Engineering ; Metabolic Flux Analysis ; Models, Biological

Owing to the worldwide obesity epidemic and the sedentary lifestyle in industrialized countries, the number of people with metabolic diseases is explosively increasing. Magnetic resonance spectroscopy (MRS), which is fundamentally similar to magnetic resonance imaging, can detect metabolic changes in vivo noninvasively. With its noninvasive nature, 1H, 13C and 31P MRS are being actively utilized in clinical and biomedical metabolic studies to detect lipids and important metabolites without ionizing radiation. 1H MRS can quantify lipid content in liver and muscle and can detect other metabolites, such as 2-hydroxyglutarate, in vivo. Of interest, many studies have indicated that hepatic and intramyocellular lipid content is inversely correlated with insulin sensitivity in humans. Thus, lipid content can be utilized as an in vivo biomarker for detecting early insulin resistance. Employing 13C MRS, hepatic glycogen synthesis and breakdown can be directly detected, whereas 31P MRS provides in vivo adenosine triphosphate (ATP) synthesis rates by saturation transfer methods in addition to ATP content. These in vivo data can be very difficult to assess by other methods and offer a critical piece of metabolic information. To aid the reader in understanding these new methods, fundamentals of MRS are described in this review in addition to promising future applications of MRS and its limitations.
Carbon-13 Magnetic Resonance Spectroscopy ; Humans ; Magnetic Resonance Imaging/methods ; *Magnetic Resonance Spectroscopy/methods ; Metabolic Diseases/*diagnosis ; Phosphorus Isotopes ; Protons

Most main oilfields in China have already entered a "double high" development stage (high water cut, high recovery degree). To further enhance oil recovery in reservoirs after polymer flooding (RAPFs), an efficient activator formulation for promoting metabolism of endogenous microorganism was studied by aerogenic experiments, physical simulation experiments, electron microscopy scanning and pyrophosphate sequencing. Results show that the activator could activate the endogenous microorganisms in the injected water and make the pressurized gas reach 2 MPa after 60 d static culture of the activator in a high pressure vessel. The oil recovery efficiency of natural core physical simulation flooding can be improved by more than 3.0% (OOIP) in RAPFs when injected 0.35 PV activator with 1.8% mass concentration, and a lot of growth and reproduction of activated endogenous microorganism in the core was observed by electron microscopy scanning. Field trial with 1 injector and 4 producers was carried out in the east of south II block of Sa Nan in December 2011. By monitoring four effective production wells, changes of carbon isotope δ13C (PDB) content of methane and carbon dioxide were -45 per thousand to -54 per thousand and 7 per thousand to 12 per thousand. Compared with east II of Sa Nan block, the oil amount increased by 35.9%, water cut stabled at 94%. The incremental oil was 5 957 t during the three and a half years, which provides an alternative approach for further improving oil recovery in similar reservoirs.
Carbon Dioxide ; chemistry ; Carbon Isotopes ; analysis ; China ; Diphosphates ; chemistry ; Methane ; chemistry ; Oil and Gas Fields ; microbiology ; Polymers ; Water ; Water Microbiology

The aim of this study is to develop a synthetic medium suitable for 13C metabolic flux analysis (13C-MFA) of Streptomyces rimosus. The cell growth rate and oxytetracycline production by S. rimosus M4018 were compared when M4018 cells were growth on the optimized chemically defined media with organic nitrogen sources or inorganic nitrogen sources. First, a synthetic medium contained KNO3 as the main nitrogen source was screened, then optimized by a response surface method. Using this new medium, the oxytetracycline yield was increased from 75.2 to 145.6 mg/L. Furthermore, based on the 13C-MFA, we identified that Entner-Doudoroff pathway does not exist in S. rimosus cells cultured in a chemically defined medium with feed of 100% 1-13C labeled glucose. This study is helpful for subsequent 13C-MFA application of S. rimosus.
Carbon Isotopes ; analysis ; Culture Media ; chemistry ; Metabolic Flux Analysis ; Nitrogen ; chemistry ; Oxytetracycline ; biosynthesis ; Streptomyces rimosus ; metabolism

Gene expression is regulated by different transcriptional regulators. The transcriptional regulator isocitrate lyase regulator (IclR) of Escherichia coli represses the expression of the aceBAK operon that codes for the glyoxylate pathway enzymes. In this study, physiological and metabolic responses of the deletion of the ic1R gene in E. coli BW25113 were investigated based on the quantification and analysis of intracellular metabolic fluxes. The knockout of the iclR gene resulted in a decrease in the growth rate, glucose uptake rate and the acetate secretion rate, but a slight increase in biomass yield. The latter could be attributed to the lowered metabolic fluxes through several CO2 generating pathways, including the redirection of 33% of isocitrate directly to succinate and malate without CO2 production as well as the reduced flux through the pentose phosphate pathway. Furthermore, although the glyoxylate shunt was activated in the iclR mutant, the flux through phosphoenolpyruvate (PEP) carboxykinase kept almost unchanged, implying an inactive PEP-glyoxylate cycle and no extra loss of carbon atoms in the mutant strain. Both the reduced glucose uptake rate and the active glyoxylate shunt were responsible for the minor decrease in acetate secretion in the ic1R knockout strain compared to that in the wild-type E. coli strain.
Carbon Isotopes ; metabolism ; Escherichia coli ; enzymology ; genetics ; Escherichia coli Proteins ; genetics ; metabolism ; Gene Knockout Techniques ; Isocitrate Lyase ; genetics ; metabolism ; Metabolic Networks and Pathways ; genetics ; Repressor Proteins ; genetics ; metabolism

BACKGROUND/AIMS: Revaprazan (Revanex(R)) is a novel proton pump inhibitor (PPI) that has a somewhat different effect on proton pump compared with the other PPI's, also (called as 'acid pump antagonist'). We aimed to examine the false negative rate of 13C-urea breath test (UBT) in the patients with Helicobacter pylori (H. pylori) associated peptic ulcer disease who were treated with revaprazan and evaluate the anti-urease activity of revaprazan. METHODS: Total 55 patients were enrolled in this study. They received EGD examination between January 2009 and December 2009 and diagnosed histologically as H. pylori associated peptic ulcer disease. All patients took revaprazan only. Three patients were excluded because of underlying chronic disease and inappropriate breath sampling. The remaining 52 patients had UBT at 0, 2 and 4 weeks of revaprazan use. After 2 weeks of the cessation of revaprazan, they had the fourth UBT. RESULTS: At 2 and 4 weeks, the false negative rates of UBT were 5.8% and 23.1%, respectively (p=0.05). After 2 weeks of the cessation, the cases of the false negative result were five. Four out of five patients had prolonged negative results on two or three successive tests, and baseline 13C difference value did not predict the false negative results. CONCLUSIONS: False negative results of UBT were common and increased with prolonged use of acid pump antagonist. As PPI, it had also anti-urease activity and most patients (47/52, 90.4%) reverted to positive results by 2 weeks after the cessation of taking the medication.
*Breath Tests ; Carbon Isotopes ; False Negative Reactions ; Female ; Helicobacter Infections/complications/*diagnosis ; *Helicobacter pylori ; Humans ; Male ; Middle Aged ; Peptic Ulcer/*drug therapy/microbiology ; Proton Pump Inhibitors/*therapeutic use ; Pyrimidinones/*therapeutic use ; Tetrahydroisoquinolines/*therapeutic use ; Urea/*diagnostic use

No abstract available.
*Breath Tests ; Carbon Isotopes ; False Negative Reactions ; Helicobacter Infections/complications/*diagnosis ; *Helicobacter pylori ; Humans ; Peptic Ulcer/*drug therapy/microbiology ; Proton Pump Inhibitors/*therapeutic use ; Pyrimidinones/*therapeutic use ; Tetrahydroisoquinolines/*therapeutic use ; Urea/*diagnostic use

In the structural determination of natural glycosides, nuclear magnetic resonance (NMR) is an important approach in determining the configuration of glycoside bond. The test of coupling constant of the anomeric proton and chemical shift of the anomeric carbon are two common methods, but these methods are not suitable for some sugars. For those sugars, detailed 13C NMR analysis is an alternative choice. This paper summarizes the characteristics of 1H and 13C NMR data of the common monosaccharides published in the literatures, in order to search an approach to determine the configuration of glycoside bond.
Carbohydrate Conformation ; Carbon Isotopes ; Glycosides ; chemistry ; Magnetic Resonance Spectroscopy ; methods ; Monosaccharides ; chemistry

The purpose of the present study is to use beta-cyclodextrin polymers (beta-CDP) with different cross-linked degree (CLD) to form inclusion complexes with ibuprofen and examine the effects of structural and compositional factors of beta-CDP on its drug loading and release behaviors. A series of beta-CDP with different CLD were synthesized and characterized by Fourier Transform Infrared Spectroscopy (FT-IR) and 13C NMR spectrum. The beta-CDP was systemically characterized for the relation between the CLD of beta-CDP and the drug loading and release as well. The results of FT-IR and 13C NMR showed that similar peak-shaped vibration of beta-CDP and beta-CD implies that the polymer keeps the original characteristic structure of beta-CD. The CLD of the beta-CDP played a critical role in the drug loading and release, increasing the CLD resulted in reduction of drug loading, but increase in drug release.
Carbon Isotopes ; Cross-Linking Reagents ; chemistry ; Delayed-Action Preparations ; Drug Carriers ; Drug Compounding ; Drug Delivery Systems ; Ibuprofen ; administration & dosage ; chemistry ; Magnetic Resonance Spectroscopy ; Pharmaceutical Preparations ; administration & dosage ; chemistry ; Polymers ; chemistry ; Solubility ; Spectroscopy, Fourier Transform Infrared ; beta-Cyclodextrins ; chemistry