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

Humans ; Isotope Labeling ; Nuclear Magnetic Resonance, Biomolecular ; Protein Domains ; src-Family Kinases ; chemistry

This study aims to develop a liquid chromatography with tandem mass spectrometry (LC-MS/MS) method for the simultaneous determination of ivabradine and N-demethylivabradine in human plasma, and investigate effects of stable isotope labeled (SIL) internal standard (IS) on ivabradine. The analytes and IS were extracted from plasma by protein precipitation with acetonitrile, and chromatographied on a Capcell PAK C18 (100 mm x 4.6 mm, 5 μm) column using a mobile phase of methanol and 5 mmol x L(-1) ammonium acetate. Multiple reaction monitoring with electrospray ionization (ESI) was used in the positive mode for mass spectrometric detection. The effect of ivabradine isotope peak [M+H+3] + on IS and the effect of SIL IS purity on ivabradine were evaluated. An appropriate concentration of SIL IS was chosen to permit method selectivity and linearity of the assay over the required range. The standard curves were demonstrated to be linear in the range of 0.100 to 60.0 ng x mL(-1) for ivabradine, and 0.050 0 to 20.0 ng x mL(-1) for N-demethylivabradine. The intra and inter day precision and accuracy were within the acceptable limits for all concentrations. Besides, the interaction between IS and ivabradine did not impact the determination of analytes. This method was successfully applied to a pharmacokinetic study of hydrogen sulfate ivabradine sustained release tablets on Chinese healthy volunteers.
Benzazepines ; blood ; Chromatography, High Pressure Liquid ; Delayed-Action Preparations ; Humans ; Isotope Labeling ; standards ; Reference Standards ; Reproducibility of Results ; Sensitivity and Specificity ; Spectrometry, Mass, Electrospray Ionization ; Tablets ; Tandem Mass Spectrometry

OBJECTIVETo test the efficiency of transfecting (99)Tc(m)-labeled anti-miR208b oligonucleotide into early hypertrophic cardiac myocytes in vitro.

METHODSThe anti-oligonucleotide targeting miR208b (AMO) was synthesized and modified with LNA followed by conjugation with N-hydroxysuccinimidyl S-acetyl-meraptoacetyl triglycine (NHS-MAG3) and radiolabeling with (99)Tc(m). NHS-MAG3-LNA-AMO and labeled AMO were purified with Sep-Pak C18 column chromatography, and the former was examined for UV absorption at the 260 nm using Gene Quant DNA/RNA calculator. The labeling efficiency, radiochemical purity, stability and molecular hybridization activity were analyzed. An angiotensin II-induced cell model of hypertrophic cardiac myocytes was transfected with (99)Tc(m)-NHS-MAG3-LNA-AMO via liposome, and the relative expression of miRNA208b and retention ratio of the labeled AMO in early hypertrophic cells were determined.

RESULTSThe labeling efficiency and radiochemical purity of the labeled AMO after purification exceeded 84% and 86%, respectively. The radio- chemical purities of the labeled AMO incubated in serum and normal saline for 12 h were both higher than 80%, and the labeled AMO showed a capacity to hybridize with the target gene. In the hypertrophic model of cardiac myocytes, the retention ratio of labeled AMO at 6 h was higher than 20%.

CONCLUSIONThe (99)Tc(m)-labeled antisense probe can be efficiently transfected into hypertrophic cardiac myocytes in vitro, which provides an experimental basis for subsequent radionuclide imaging studies.

Humans ; Isotope Labeling ; Liposomes ; MicroRNAs ; genetics ; Myocytes, Cardiac ; Oligonucleotides ; Oligonucleotides, Antisense ; Oligopeptides ; Radiopharmaceuticals ; Silicon Dioxide ; Succinimides ; Transfection

Histone deacetylase 6 (HDAC6), a predominantly cytoplasmic protein deacetylase, participates in a wide range of cellular processes through its deacetylase activity. However, the diverse functions of HDAC6 cannot be fully elucidated with its known substrates. In an attempt to explore the substrate diversity of HDAC6, we performed quantitative proteomic analyses to monitor changes in the abundance of protein lysine acetylation in response to HDAC6 deficiency. We identified 107 proteins with elevated acetylation in the liver of HDAC6 knockout mice. Three cytoplasmic proteins, including myosin heavy chain 9 (MYH9), heat shock cognate protein 70 (Hsc70), and dnaJ homolog subfamily A member 1 (DNAJA1), were verified to interact with HDAC6. The acetylation levels of these proteins were negatively regulated by HDAC6 both in the mouse liver and in cultured cells. Functional studies reveal that HDAC6-mediated deacetylation modulates the actin-binding ability of MYH9 and the interaction between Hsc70 and DNAJA1. These findings consolidate the notion that HDAC6 serves as a critical regulator of protein acetylation with the capability of coordinating various cellular functions.
Acetylation ; Actins ; chemistry ; metabolism ; Animals ; Cell Line ; Chromatography, High Pressure Liquid ; HSC70 Heat-Shock Proteins ; metabolism ; HSP40 Heat-Shock Proteins ; metabolism ; Histone Deacetylase 6 ; Histone Deacetylases ; metabolism ; Isotope Labeling ; Liver ; metabolism ; Lysine ; metabolism ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Microscopy, Confocal ; Nonmuscle Myosin Type IIA ; metabolism ; Protein Binding ; Proteomics ; Substrate Specificity ; Tandem Mass Spectrometry

The stable isotope labeling by amino acids in culture (SILAC) based quantitative proteomics serves as a gold standard because of the high accuracy and throughput for protein identifications and quantification. In this study, we discussed the application of SILAC technology in mammal model, and developed quantitative internal standard for comparative proteomics of disease model. The C57BL/6J mice fed by special diet containing the 13C6-Lysine and bred F2 generation. We identified and analyzed total proteins of 9 mice tissues of F2 generation, including brain, lung, heart, stomach, intestine, liver, spleen, kidney, and muscle. Quantitative analysis information could evaluate the mice and different tissues' labeling efficiency. Liver was the most efficient, brain the least, and the labeling efficiency were 96.34%±0.90% and 92.62%±1.98% respectively. The average of the labeling efficiency of F2 generation was 95.80%±0.64%, which met the international standard (≥ 95%) for SILAC quantitative proteomics effective study. SILAC technology was successfully extended to mammalian model system, which will provide powerful tools for the mechanism study of the pathophysiology process with mouse model.
Amino Acids ; chemistry ; Animals ; Diet ; veterinary ; Isotope Labeling ; Lysine ; chemistry ; Mice ; Mice, Inbred C57BL ; Proteins ; chemistry ; Proteomics ; methods

BACKGROUNDThe glucose fluxes of individuals with prediabetes in Chinese population are not clear. This study was to determine whether the endogenous glucose production (EGP), oral glucose rate of appearance (Ra) and glucose rate of disappearance (Rd) were different in Chinese individuals with prediabetes under fasting conditions and following an oral glucose challenge.

METHODSFive subjects with type 2 diabetes, 5 subjects with prediabetes and 5 non-diabetic subjects matched for age, weight, fat free mass and body mass index underwent a 180 minute stable glucose isotope tracing ([6, 6-(2)H2] glucose, [1-(13)C] glucose, and [U-(13)C] glucose) study under fasting and after ingestion of a 75 g oral glucose load. Isotope glucose enrichment was measured by gas chromatography-mass spectrometry. Insulin sensitivity was estimated using the oral glucose tolerance test (OGTT)-derived insulin sensitivity index, β cell function was determined by the insulinogenic index (δI30/δG30).

RESULTSThe insulin sensitivity index (P = 0.043) and insulinogenic index (P = 0.021) were decreased in subjects with prediabetes compared with non-diabetes. Fasting EGP was slightly higher (P = 0.29) and postprandial EGP was comparable in subjects with prediabetes and non-diabetes during 120 minutes after glucose ingestion, but nadir EGP occurred later in prediabetic than non-diabetic subjects. Ra did not differ among the three groups. Rd was substantially lower in subjects with prediabetes than non-diabetes after glucose intake (P = 0.013).

CONCLUSIONThe mild hyperglycemia observed among individuals with prediabetes may result from decreased Rd during the postprandial state.

Blood Glucose ; metabolism ; Case-Control Studies ; Diabetes Mellitus, Type 2 ; blood ; Fasting ; blood ; Female ; Glucose ; metabolism ; Glucose Tolerance Test ; Humans ; Hyperglycemia ; blood ; Isotope Labeling ; Male ; Middle Aged ; Prediabetic State ; blood

OBJECTIVETo evaluate the iron utilization in children using single stable isotopes tracer.

METHODS57 children aged from 10 to 12 from a primary school of Beijing in 2010 were selected, 30 of them were boys and 27 were girls. All the subjects were given 5 ml artificial enriched ⁵⁷FeSO₄ twice per day within 5 days, and the total amount of ⁵⁷Fe was 30 mg. 5 ml blood were taken at 1 day before and 14 days after test, and all the feces during the test were collected. The samples were detected by AAS and MC-ICP-MS after pre-treatment to determine the content and abundances of iron in samples, then the iron utilization in whole blood were calculated.

RESULTSThe blood volume of male and female subjects 14 days after test were (3.19 ± 0.41) and (3.15 ± 0.29) ml respectively, and there was no significantly difference (t = 1.13, P > 0.05) between them; The amount of ⁵⁷Fe intake by male and female subjects were (27.46 ± 0.25) and (27.29 ± 0.15) mg (t = 1.13, P > 0.05); The amount of ⁵⁷Fe in blood were (5.92 ± 0.71) and (6.30 ± 0.65) mg respectively (t = 2.29, P < 0.05); The iron utilization in whole blood at 14 days of male and female subjects were (20.41 ± 2.03)% and (22.04 ± 0.80)% respectively, male subjects were significantly lower than females (t = 2.51, P < 0.05).

CONCLUSIONSingle stable isotopes tracer can be used in iron utilization evaluation in children, and the iron utilization in whole blood of female children is higher than males.

Biological Availability ; Child ; Female ; Humans ; Iron ; blood ; Isotope Labeling ; methods ; Male

OBJECTIVETo analysis the molecular interaction network of 14-3-3 sigma in non small cell lung cancer (NSCLC) cells.

METHODSEstablished stable over-expressed 14-3-3 sigma protein PG cells, MTT assay was used to assess the growth rate of PG cells. Though stable isotope labeling by amino acids in cell culture (SILAC) and Mass spectrometry (MS) technology, to identify difference expressed proteins caused by over expressed 14-3-3 sigma. The protein expressed >2 or <0.5 times was termed as the differential protein. By searching Human protein reference database (HPRD) and Kyoto encyclopedia of genes and genomes (KEGG), established the molecular interaction network of tumor suppressor gene 14-3-3 sigma.

RESULTSThe growth rate of over-expressed 14-3-3 sigma PG cell was obviously slower down compared to vector PG cells. A database including 147 differential protein was established. And a molecular interaction network of 14-3-3 sigma containing 26 protein was constructed.In this network, the expression of CSNK2A1 (casein kinase II subunit alpha), involved in numerous cellular processes, such as cell cycle progression, apoptosis and transcription, was the most significantly increased. A DNA repair protein, MEN1 (Menin) which functions as a transcriptional regulator was the most significantly decreased.

CONCLUSIONAfter stable transfected with 14-3-3 sigma gene, growth rate of PG cells was inhibited, the proteins associated with cell cycle, DNA damage repair mechanisms were significantly changed, and constructed the molecular interaction network.

14-3-3 Proteins ; genetics ; Amino Acids ; Biomarkers, Tumor ; genetics ; Carcinoma, Non-Small-Cell Lung ; genetics ; Cell Cycle ; Cell Line, Tumor ; Cell Proliferation ; Exoribonucleases ; genetics ; Humans ; Isotope Labeling ; methods ; Lung Neoplasms ; genetics ; Mass Spectrometry ; Transfection